MEMBRANE PROTEIN SIMULATION: GLIC¶
Setting up membrane protein simulations is trickier than preparing a soluble protein. However the basic needs are the same. Meaning that you need coordinate files (protein and lipid) and the corresponding topologies. Forcefield files and the topology of lipids is provided within the tuturial files you will download below. The tutorial is a bit long. But I wanted to explain the steps to a person who is not familiar with the process at all.
Before we start lets create a project directory named GLIC_pH70. The protein we are going to use, as the name of the folder states, is called GLIC. GLIC is a pH-gated cationic channel, homologous to cys-loop receptors. pH-gated here means the activation is done by increasing the pH from 7.0 to 4.0. There for we named the folder pH70. After you have gone through this tutorial and enjoyed it, you can try changing the protonation states of some residues and setup another simulation as a practice. Back to business…
Now within GLIC_pH70 create the following folders: prep, run-files, em, equi, prod. prep folder is our working directory to setup the simulation box. run-files is the directy we will place the final files. In theory this is just a duplication of the files within prep but things gets messy there. So it is a good practice to have a clean copy of the basic files in a seperate folder. em, equi, and prod folders will contain the minimisation, equilibration and the production runs.
PREREQUISITES¶
Even if setting up simulations is not your main job, you clearly felt the need to setup a simulation or two that you have ended up going through this page. I strongly recommend getting familiar with the basic terminal commands. If you are an experimentalit, it might be a scary transition. But the tasks are much easier to complete!!! Trust me I have done that transition. There is nothing to fear. Just don’t use the remove/move commands with a *. You are more than welcomed to contact me for help.
Also I assume you know the meaning of a simulation. If not, I do not recemmonned starting with membrane proteins. Setting up a membrane protein simulation right away could be frusturating due to extra steps required to prepare. Justin Lemkul’s tutorials are a perfect way to start.
Now the real requirements: You should have VMD and GROMACS installed. If you are using terminal (bash) set the variables below and source the gromacs if it is not in your path:
[ ]:
#This is a python cell, the rest of the cells are bash. Do not run this cell.
#If you are on terminal use the commented out cells below for setting the environment.
#export VMD=/path/to/your/vmd_executable
#source /path/to/your/gmx/bin/GMXRC
[1]:
%%bash
#If you are running this as a jupyter notebook run the command below to set the aliases.
#You must also uncomment the lines on top of each cell
#echo 'export VMD="/path/to/your/vmd_executable"' >> sources.sh
#echo 'source /path/to/your/gmx/bin/GMXRC' >> sources.sh
echo "export VMD=/Applications/VMD1.9.2.app/Contents/vmd/vmd_MACOSXX86" >> sources.sh
echo "source /usr/local/gromacs/bin/GMXRC" >> sources.sh
PREPARE THE COORDINATES AND THE TOPOLOGY¶
Go a head and download the tutorial files and extract. Within the extracted folder you will find two forcefield folders. It’s better if you don’t make modifications to the main gromacs forcefield folder in the beginning. So keep these folders here for now, even tough one of those folder is a duplication of what is already installed. Move them over to the prep folder. Both of them are needed! One is the original amber99sb-ILDN folder. The other one is extended with the lipid parameters.
I have provided two coordinate files ending with .pdb. 4NPQ_BA1.pdb is the first biological assembly of the GLIC 4NPQ structure. Crystal structures often contain other molecules than protein or missing residues/atoms. I have cleaned the crystal structure from extra molecules and other biological assemblies. Then used MODELLER to fix the missing backbone&sidechain atoms. There are other ways to fix the structure. But these will not be covered in this tutorial. The second coordinate file contains Berger POPC lipids. It is a bilayer with 332 lipids. This lipid patch is just enough size to accomodate GLIC. Copy both files to prep folder.
You will also find a .tcl script and gmembed.mdp, gmembed.dat files. Copy these to the prep folder too. I will explain their job below. There are some limitations when we use bash magic cells. You can run the commands in a terminal or close the notebook, move it to prep folder and open it again. This way you should be able to run the cells directly.
Now the real fun begins; load these two structures to your favorite visualization software. You see that these two structures are not aligned. In order to place the protein into the membrane first we need to align them. Our membrane patch expands on the xy plane. That means we need to align the transmembrane domain to its 3rd principal axis, z.
If you are adventurous you can try to do this manually :-) If you want to a short cut here are some awesome tools from gromacs and a beatiful VMD script. 1. First we align the protein on its principal axes and center it at 0 0 0 2. Next we rotate it by 90° around the y axis. These steps aligns the protein channel with the z axis. It also enables us to place the transmembrane domain to the bilayer correctly. 3. As the last step we move/translate the protein into the bilayer. The .tcl script moves the protein by aligning the the center of the trasmembrane domain to the center of the bilayer.
[2]:
%%bash
source sources.sh
gmx editconf -f 4NPQ_BA1.pdb -o GLIC_princ.pdb -center 0 0 0 -princ <<EOF
1
EOF
gmx editconf -f GLIC_princ.pdb -o GLIC_princ_rotate.pdb -rotate 0 90 0
$VMD -dispdev text -e protein_center_to_lipids.tcl -args GLIC_princ_rotate.pdb popc_332.pdb GLIC_princ_rotate_translate
Read 12630 atoms
No velocities found
system size : 11.743 8.491 11.801 (nm)
center : -5.427 -1.985 -0.176 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
Selected 1: 'Protein'
new system size : 11.374 8.379 8.278
shift : 5.426 1.985 0.173 (nm)
new center : -0.000 0.000 -0.000 (nm)
new box vectors : 0.000 0.000 0.000 (nm)
new box angles : 0.00 0.00 0.00 (degrees)
new box volume : 0.00 (nm^3)
Read 12630 atoms
No velocities found
system size : 11.375 8.379 8.278 (nm)
center : -0.000 0.000 -0.000 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
Rotating 0, 90, 0 degrees around the X, Y and Z axis respectively
new system size : 8.278 8.379 11.375
new center : -0.000 0.000 0.000 (nm)
Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd@ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD1.9.2.app/Contents/vmd/plugins/MACOSXX86/molfile
The drugui package could not be loaded:
/Applications/VMD1.9.2.app/Contents/vmd/scripts/tcl8.5 /Applications/VMD1.9.2.app/Contents/vmd/scripts /Applications/VMD1.9.2.app/Contents/lib /Applications/VMD1.9.2.app/Contents/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts ~/Library/Tcl /Library/Tcl /Network/Library/Tcl /System/Library/Tcl ~/Library/Frameworks /Library/Frameworks /Network/Library/Frameworks /System/Library/Frameworks /Applications/VMD1.9.2.app/Contents/vmd/scripts/vmd /Applications/VMD1.9.2.app/Contents/vmd/plugins/MACOSXX86/tcl /Applications/VMD1.9.2.app/Contents/vmd/plugins/noarch/tcl /System/Library/Tcl/8.5 /System/Library/Tcl/tcllib1.12 /System/Library/Tcl/tklib0.5 /System/Library/Tcl/8.5/vfs1.4.1/template ~/Documents/scripts/la1.0
/Applications/VMD1.9.2.app/Contents/vmd/scripts/tcl8.5 /Applications/VMD1.9.2.app/Contents/vmd/scripts /Applications/VMD1.9.2.app/Contents/lib /Applications/VMD1.9.2.app/Contents/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts ~/Library/Tcl /Library/Tcl /Network/Library/Tcl /System/Library/Tcl ~/Library/Frameworks /Library/Frameworks /Network/Library/Frameworks /System/Library/Frameworks /Applications/VMD1.9.2.app/Contents/vmd/scripts/vmd /Applications/VMD1.9.2.app/Contents/vmd/plugins/MACOSXX86/tcl /Applications/VMD1.9.2.app/Contents/vmd/plugins/noarch/tcl /System/Library/Tcl/8.5 /System/Library/Tcl/tcllib1.12 /System/Library/Tcl/tklib0.5 /System/Library/Tcl/8.5/vfs1.4.1/template ~/Documents/scripts/la1.0 ~/Documents/scripts/orient
Info) Using plugin pdb for structure file GLIC_princ_rotate.pdb
Info) Using plugin pdb for coordinates from file GLIC_princ_rotate.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 12630
Info) Bonds: 13192
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1555
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 5 Protein: 5 Nucleic: 0
Info) Finished with coordinate file GLIC_princ_rotate.pdb.
0
Info) Using plugin pdb for structure file popc_332.pdb
Info) Using plugin pdb for coordinates from file popc_332.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 77024
Info) Bonds: 56772
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 20252
Info) Waters: 19920
Info) Segments: 1
Info) Fragments: 20252 Protein: 0 Nucleic: 0
Info) Finished with coordinate file popc_332.pdb.
1
atomselect0
atomselect1
atomselect2
51.74549865722656 52.776763916015625 45.45720672607422
0.14343200623989105 0.09072847664356232 -29.331968307495117
51.60206665098667 52.68603543937206 74.78917503356934
51.60206665098667 52.68603543937206 74.78917503356934
Info) Opened coordinate file GLIC_princ_rotate_translate.pdb for writing.
Info) Finished with coordinate file GLIC_princ_rotate_translate.pdb.
Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)
Info) Exiting normally.
:-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx editconf -f 4NPQ_BA1.pdb -o GLIC_princ.pdb -center 0 0 0 -princ
Select group for the determining the orientation
Group 0 ( System) has 12630 elements
Group 1 ( Protein) has 12630 elements
Group 2 ( Protein-H) has 12630 elements
Group 3 ( C-alpha) has 1555 elements
Group 4 ( Backbone) has 4665 elements
Group 5 ( MainChain) has 6225 elements
Group 6 ( MainChain+Cb) has 7750 elements
Group 7 ( MainChain+H) has 6225 elements
Group 8 ( SideChain) has 6405 elements
Group 9 ( SideChain-H) has 6405 elements
Select a group:
Back Off! I just backed up GLIC_princ.pdb to ./#GLIC_princ.pdb.1#
GROMACS reminds you: "I'm Gonna Get Medieval On Your Ass" (Pulp Fiction)
:-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx editconf -f GLIC_princ.pdb -o GLIC_princ_rotate.pdb -rotate 0 90 0
Back Off! I just backed up GLIC_princ_rotate.pdb to ./#GLIC_princ_rotate.pdb.1#
GROMACS reminds you: "The time for theory is over" (J. Hajdu)
If you load the output generated with above commands to a visualisation software, you will be able to understand better what each steps does.
Now we have our protein placed at the same plane as our bilayer. However they are still two seperate files. Before we concatanate them, we need to process the protein file further and obtain a topology file for it. For lipids we already have the topology files within the forcefield directory. pdb2gmx is the tool in GMX that creates the protein topologies for us. Since we want to run a GLIC simulation at pH 7.0, no need to assign different protonation states (protonation states of histidines are tricky but we will go with default assignments for now). pdb2gmx will ask for (1) a forcefield choice and (2) a water model. When prompted choose 1 (corresponds to amber99s-ildn_berger forcefield) and 1 (TIP3P water model).
[3]:
%%bash
source sources.sh
gmx pdb2gmx -f GLIC_princ_rotate_translate.pdb -o GLIC_pH70.pdb -ignh -vsite hydrogens <<EOF
1
1
EOF
Select the Force Field:
From current directory:
1: AMBER99SB-ILDN force field, extended with Berger united-atom lipids
2: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
From '/usr/local/gromacs/share/gromacs/top':
3: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
5: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
6: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
7: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
8: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
10: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
11: CHARMM36 all-atom force field (March 2017)
12: GROMOS96 43a1 force field
13: GROMOS96 43a2 force field (improved alkane dihedrals)
14: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
15: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
16: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Using the Amber99sb-ildn-berger force field in directory ./amber99sb-ildn-berger.ff
Select the Water Model:
Reading GLIC_princ_rotate_translate.pdb...
Read 12630 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 5 chains and 0 blocks of water and 1555 residues with 12630 atoms
chain #res #atoms
1 'A' 311 2526
2 'B' 311 2526
3 'C' 311 2526
4 'D' 311 2526
5 'E' 311 2526
Reading residue database... (amber99sb-ildn-berger)
Processing chain 1 'A' (2526 atoms, 311 residues)
Identified residue VAL5 as a starting terminus.
Identified residue PHE315 as a ending terminus.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 311 residues with 5074 atoms
Chain time...
Processing chain 2 'B' (2526 atoms, 311 residues)
Identified residue VAL5 as a starting terminus.
Identified residue PHE315 as a ending terminus.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 311 residues with 5074 atoms
Chain time...
Processing chain 3 'C' (2526 atoms, 311 residues)
Identified residue VAL5 as a starting terminus.
Identified residue PHE315 as a ending terminus.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 311 residues with 5074 atoms
Chain time...
Processing chain 4 'D' (2526 atoms, 311 residues)
Identified residue VAL5 as a starting terminus.
Identified residue PHE315 as a ending terminus.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 311 residues with 5074 atoms
Chain time...
Processing chain 5 'E' (2526 atoms, 311 residues)
Identified residue VAL5 as a starting terminus.
Identified residue PHE315 as a ending terminus.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 311 residues with 5074 atoms
Chain time...
Including chain 1 in system: 5554 atoms 311 residues
Including chain 2 in system: 5554 atoms 311 residues
Including chain 3 in system: 5554 atoms 311 residues
Including chain 4 in system: 5554 atoms 311 residues
Including chain 5 in system: 5554 atoms 311 residues
--------- PLEASE NOTE ------------
You have successfully generated a topology from: GLIC_princ_rotate_translate.pdb.
The Amber99sb-ildn-berger force field and the tip3p water model are used.
--------- ETON ESAELP ------------
:-) GROMACS - gmx pdb2gmx, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx pdb2gmx, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx pdb2gmx -f GLIC_princ_rotate_translate.pdb -o GLIC_pH70.pdb -ignh -vsite hydrogens
Opening force field file ./amber99sb-ildn-berger.ff/watermodels.dat
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.r2b
Opening force field file ./amber99sb-ildn-berger.ff/dna.r2b
Opening force field file ./amber99sb-ildn-berger.ff/rna.r2b
All occupancies are one
Opening force field file ./amber99sb-ildn-berger.ff/atomtypes.atp
Atomtype 67
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file ./amber99sb-ildn-berger.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file ./amber99sb-ildn-berger.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.hdb
Opening force field file ./amber99sb-ildn-berger.ff/dna.hdb
Opening force field file ./amber99sb-ildn-berger.ff/rna.hdb
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.n.tdb
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 460 donors and 453 acceptors were found.
There are 644 hydrogen bonds
Will use HISE for residue 127
Will use HISE for residue 235
Will use HISE for residue 277
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS27 HIS127 MET205 HIS235 MET252 MET261
SG168 NE2991 SD1631 NE21874 SD2012 SD2082
HIS127 NE2991 1.444
MET205 SD1631 2.852 3.020
HIS235 NE21874 3.216 3.304 0.506
MET252 SD2012 2.862 2.414 1.368 1.311
MET261 SD2082 3.464 3.155 1.137 1.123 1.163
HIS277 NE22219 5.780 5.765 2.973 2.568 3.421 2.814
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-berger.ff/dna.arn
Opening force field file ./amber99sb-ildn-berger.ff/rna.arn
Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.1#
Making bonds...
Number of bonds was 5143, now 5142
Marked 2548 virtual sites
Added 480 dummy masses
Added 777 new constraints
Generating angles, dihedrals and pairs...
Before cleaning: 13589 pairs
Before cleaning: 14199 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14199 dihedrals, 1038 impropers, 9309 angles
13460 pairs, 5142 bonds and 2731 virtual sites
Total mass 35605.305 a.m.u.
Total charge -6.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.1#
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 460 donors and 453 acceptors were found.
There are 653 hydrogen bonds
Will use HISE for residue 127
Will use HISE for residue 235
Will use HISE for residue 277
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS27 HIS127 MET205 HIS235 MET252 MET261
SG168 NE2991 SD1631 NE21874 SD2012 SD2082
HIS127 NE2991 1.450
MET205 SD1631 2.856 3.021
HIS235 NE21874 3.183 3.284 0.403
MET252 SD2012 2.887 2.430 1.363 1.340
MET261 SD2082 3.474 3.163 1.138 1.091 1.152
HIS277 NE22219 5.798 5.781 2.983 2.624 3.423 2.823
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-berger.ff/dna.arn
Opening force field file ./amber99sb-ildn-berger.ff/rna.arn
Back Off! I just backed up topol_Protein_chain_B.itp to ./#topol_Protein_chain_B.itp.1#
Making bonds...
Number of bonds was 5143, now 5142
Marked 2548 virtual sites
Added 480 dummy masses
Added 777 new constraints
Generating angles, dihedrals and pairs...
Before cleaning: 13589 pairs
Before cleaning: 14199 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14199 dihedrals, 1038 impropers, 9309 angles
13460 pairs, 5142 bonds and 2731 virtual sites
Total mass 35605.305 a.m.u.
Total charge -6.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_B.itp to ./#posre_Protein_chain_B.itp.1#
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 460 donors and 453 acceptors were found.
There are 640 hydrogen bonds
Will use HISE for residue 127
Will use HISE for residue 235
Will use HISE for residue 277
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS27 HIS127 MET205 HIS235 MET252 MET261
SG168 NE2991 SD1631 NE21874 SD2012 SD2082
HIS127 NE2991 1.446
MET205 SD1631 2.796 3.025
HIS235 NE21874 3.117 3.287 0.416
MET252 SD2012 2.834 2.442 1.367 1.335
MET261 SD2082 3.432 3.179 1.138 1.101 1.157
HIS277 NE22219 5.725 5.786 2.978 2.618 3.421 2.819
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-berger.ff/dna.arn
Opening force field file ./amber99sb-ildn-berger.ff/rna.arn
Back Off! I just backed up topol_Protein_chain_C.itp to ./#topol_Protein_chain_C.itp.1#
Making bonds...
Number of bonds was 5143, now 5142
Marked 2548 virtual sites
Added 480 dummy masses
Added 777 new constraints
Generating angles, dihedrals and pairs...
Before cleaning: 13589 pairs
Before cleaning: 14199 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14199 dihedrals, 1038 impropers, 9309 angles
13460 pairs, 5142 bonds and 2731 virtual sites
Total mass 35605.305 a.m.u.
Total charge -6.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_C.itp to ./#posre_Protein_chain_C.itp.1#
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 460 donors and 453 acceptors were found.
There are 651 hydrogen bonds
Will use HISE for residue 127
Will use HISE for residue 235
Will use HISE for residue 277
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS27 HIS127 MET205 HIS235 MET252 MET261
SG168 NE2991 SD1631 NE21874 SD2012 SD2082
HIS127 NE2991 1.438
MET205 SD1631 2.842 3.012
HIS235 NE21874 3.213 3.296 0.504
MET252 SD2012 2.884 2.423 1.362 1.303
MET261 SD2082 3.445 3.152 1.129 1.120 1.154
HIS277 NE22219 5.789 5.772 2.978 2.578 3.423 2.822
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-berger.ff/dna.arn
Opening force field file ./amber99sb-ildn-berger.ff/rna.arn
Back Off! I just backed up topol_Protein_chain_D.itp to ./#topol_Protein_chain_D.itp.1#
Making bonds...
Number of bonds was 5143, now 5142
Marked 2548 virtual sites
Added 480 dummy masses
Added 777 new constraints
Generating angles, dihedrals and pairs...
Before cleaning: 13589 pairs
Before cleaning: 14199 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14199 dihedrals, 1038 impropers, 9309 angles
13460 pairs, 5142 bonds and 2731 virtual sites
Total mass 35605.305 a.m.u.
Total charge -6.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_D.itp to ./#posre_Protein_chain_D.itp.1#
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 460 donors and 453 acceptors were found.
There are 643 hydrogen bonds
Will use HISE for residue 127
Will use HISE for residue 235
Will use HISE for residue 277
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS27 HIS127 MET205 HIS235 MET252 MET261
SG168 NE2991 SD1631 NE21874 SD2012 SD2082
HIS127 NE2991 1.434
MET205 SD1631 2.888 3.029
HIS235 NE21874 3.207 3.282 0.401
MET252 SD2012 2.901 2.418 1.371 1.345
MET261 SD2082 3.477 3.157 1.131 1.098 1.159
HIS277 NE22219 5.836 5.782 2.983 2.634 3.433 2.826
Opening force field file ./amber99sb-ildn-berger.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-berger.ff/dna.arn
Opening force field file ./amber99sb-ildn-berger.ff/rna.arn
Back Off! I just backed up topol_Protein_chain_E.itp to ./#topol_Protein_chain_E.itp.1#
Making bonds...
Number of bonds was 5143, now 5142
Marked 2548 virtual sites
Added 480 dummy masses
Added 777 new constraints
Generating angles, dihedrals and pairs...
Before cleaning: 13589 pairs
Before cleaning: 14199 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 14199 dihedrals, 1038 impropers, 9309 angles
13460 pairs, 5142 bonds and 2731 virtual sites
Total mass 35605.305 a.m.u.
Total charge -6.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_E.itp to ./#posre_Protein_chain_E.itp.1#
Now there are 27770 atoms and 1555 residues
Total mass in system 178026.526 a.m.u.
Total charge in system -30.000 e
Writing coordinate file...
Back Off! I just backed up GLIC_pH70.pdb to ./#GLIC_pH70.pdb.1#
GROMACS reminds you: "There's No Room For the Weak" (Joy Division)
Note that in the above command we have ignored the hydrogens within our input structure (ignh) and added new hydrogens along with virtual sites. Virtual sites are required to speed up the calculations. You can read more about it on the gromacs manual. But in simple words, it creates a ghost particle which represents the hydrogens together with heavy atoms. By doing so, we don’t have to calculate the fast vibrations of hydrogens in small intervals (timestep).
So now we have a protein structure that can be combined with the lipid file since it has the correct terminal ends
[4]:
%%bash
head -4 popc_332.pdb > GLIC_pH70_popc.pdb
grep 'ATOM' GLIC_pH70.pdb >> GLIC_pH70_popc.pdb
grep 'POPC' popc_332.pdb >> GLIC_pH70_popc.pdb
echo 'END' >> GLIC_pH70_popc.pdb
Next we create a box and solvate it. The bilayer file I have provided already contains the box dimensions required. So all we need to do is to center the system within that box and add waters. Adding waters to bilayer systems are a bit tricky, especially with channels. You want water within the channel, but you not within the bilayer. Since there is space within the bilayer, solvation tools fills it with waters. But luckily there are several work arounds to the issue. I will use the method where we increase the vdW radius of the POPC carbons.
[5]:
%%bash
source sources.sh
gmx editconf -f GLIC_pH70_popc.pdb -o GLIC_pH70_popc_center.pdb -c -bt cubic
cp /usr/local/gromacs/share/gromacs/top/vdwradii.dat b_vdwradii.dat
sed '/; Water charge sites/ a\
POP C 0.45 \
' b_vdwradii.dat > vdwradii.dat
gmx solvate -cp GLIC_pH70_popc_center.pdb -cs -o GLIC_pH70_popc_center_sol.pdb
rm vdwradii.dat
Read 45034 atoms
Volume: 1758.73 nm^3, corresponds to roughly 791400 electrons
No velocities found
system size : 12.933 12.566 11.659 (nm)
diameter : 16.346 (nm)
center : 5.165 5.272 6.341 (nm)
box vectors : 10.484 10.484 16.000 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :1758.73 (nm^3)
shift : 0.077 -0.029 1.659 (nm)
new center : 5.242 5.242 8.000 (nm)
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------
:-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx editconf -f GLIC_pH70_popc.pdb -o GLIC_pH70_popc_center.pdb -c -bt cubic
Back Off! I just backed up GLIC_pH70_popc_center.pdb to ./#GLIC_pH70_popc_center.pdb.1#
GROMACS reminds you: "You Will Be Surprised At What Resides In Your Inside" (Arrested Development)
:-) GROMACS - gmx solvate, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx solvate, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx solvate -cp GLIC_pH70_popc_center.pdb -cs -o GLIC_pH70_popc_center_sol.pdb
Reading solute configuration
Small POP_membrane
Containing 45034 atoms in 1887 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues
Initialising inter-atomic distances...
Warning double different entries POP C 0.45 and 0.17 on line 9 in file vdwradii.dat
Using last entry (0.45)
Generating solvent configuration
Will generate new solvent configuration of 6x6x9 boxes
Solvent box contains 189750 atoms in 63250 residues
Removed 16827 solvent atoms due to solvent-solvent overlap
Removed 69714 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 34403 residues
Generated solvent containing 103209 atoms in 34403 residues
Writing generated configuration to GLIC_pH70_popc_center_sol.pdb
Back Off! I just backed up GLIC_pH70_popc_center_sol.pdb to ./#GLIC_pH70_popc_center_sol.pdb.1#
Output configuration contains 148243 atoms in 36290 residues
Volume : 1758.73 (nm^3)
Density : 1003.96 (g/l)
Number of SOL molecules: 34403
GROMACS reminds you: "I was detained, I was restrained" (The Smiths)
Now take a look at the end file GLIC_pH70_popc_center_sol.pdb and make sure that the bilayer is not invaded by a ton of water molecules. Altough above method worked for me everytime, it is better to make sure then cry over a setup not working. You can play around with the radius 0.45 to get better results.
At this point we still have overlapping lipids with the protein. So if you choose to look at it with cartoon representation you will not see parts of the protein. Do not be alarmed. The protein is there! Change the representation to lines/licorice or speheres then you will see it.
If everything looks ok proceed to run g_membed to remove overlapping molecules. Since g_membed uses mdrun, we need to update the topology file to include lipids and water. After g_membed run we add more waters to the system so that the pore area previously occupied by lipids also gets hydrated. Running g_membed will take a while, don’t worry if it doesn’t finish right away. You can keep track of the process by going into the g_membed folder, and checking the log files.
[6]:
%%bash
source sources.sh
SOL_NR=`grep "OW" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1}'`
LIPID_NR=`grep "POPC" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1/52}'`
grep -v "Protein_chain_[B-E]" topol.top > GLIC_pH70_popc_sol.top
sed -i '' '/topol_Protein_chain_A.itp"/ a\
#include "amber99sb-ildn-berger.ff/popc.itp" \
' GLIC_pH70_popc_sol.top
sed -i '' 's/Protein_chain_A 1/Protein_chain_A 5/g' GLIC_pH70_popc_sol.top
echo 'POPC '$LIPID_NR >> GLIC_pH70_popc_sol.top
echo 'SOL '$SOL_NR >> GLIC_pH70_popc_sol.top
sed -i '' 's/amber99sb-ildn.ff/amber99sb-ildn-berger.ff/g' GLIC_pH70_popc_sol.top
mkdir -p g_membed
cp gmembed.mdp gmembed.dat g_membed/
cd g_membed
rm *.tpr *.pdb
touch box.mdp
gmx grompp -f box.mdp -c ../GLIC_pH70_popc_center_sol.pdb -p ../GLIC_pH70_popc_sol.top -o b4membed.tpr
gmx trjconv -f ../GLIC_pH70_popc_center_sol.pdb -o b4membed.pdb -s b4membed -ur rect -pbc mol<<EOF
0
EOF
gmx make_ndx -f ../GLIC_pH70_popc_center_sol.pdb -o index_before_gmembed.ndx<<EOF
name 13 POPC
q
EOF
gmx grompp -f gmembed.mdp -c b4membed.pdb -o gmembed.tpr -maxwarn 1 -n index_before_gmembed -p ../GLIC_pH70_popc_sol.top -v
gmx mdrun -nt 1 -s gmembed.tpr -membed gmembed.dat -c GLIC_pH70_popc_further_solvate.pdb -mn index_before_gmembed -v <<EOF
1
13
EOF
cp /usr/local/gromacs/share/gromacs/top/vdwradii.dat b_vdwradii.dat
sed '/; Water charge sites/ a\
POP C 0.45 \
' b_vdwradii.dat > vdwradii.dat
gmx solvate -cp GLIC_pH70_popc_further_solvate.pdb -cs -o GLIC_pH70_POPC_SOL.pdb
rm vdwradii.dat
Analysing residue names:
There are: 1555 Protein residues
There are: 332 Other residues
There are: 34403 Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 11 Mb of data
Select group for output
Selected 0: 'System'
Going to read 0 old index file(s)
Analysing residue names:
There are: 1555 Protein residues
There are: 332 Other residues
There are: 34403 Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 148243 atoms
1 Protein : 27770 atoms
2 Protein-H : 15030 atoms
3 C-alpha : 1555 atoms
4 Backbone : 4665 atoms
5 MainChain : 6225 atoms
6 MainChain+Cb : 7750 atoms
7 MainChain+H : 7700 atoms
8 SideChain : 20070 atoms
9 SideChain-H : 8805 atoms
10 Prot-Masses : 25370 atoms
11 non-Protein : 120473 atoms
12 Other : 17264 atoms
13 POPC : 17264 atoms
14 Water : 103209 atoms
15 SOL : 103209 atoms
16 non-Water : 45034 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
>
>
processing topology...
Largest charge group radii for Van der Waals: 0.179, 0.169 nm
Largest charge group radii for Coulomb: 0.179, 0.169 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 96x96x144, spacing 0.109 0.109 0.111
This run will generate roughly 362 Mb of data
Selected 1: 'Protein'
Selected 13: 'POPC'
The estimated area of the protein in the membrane is 30.983 nm^2
There are 281 lipids in the membrane part that overlaps the protein.
The area per lipid is 0.6584 nm^2.
Maximum number of lipids that will be removed is 94.
Will resize the protein by a factor of 0.300 in the xy plane and 1.000 in the z direction.
This resizing will be done with respect to the geometrical center of all protein atoms
that span the membrane region, i.e. z between 3.240 and 8.908
Will remove 0 Protein_chain_A molecules
Will remove 26 POPC molecules
Will remove 691 SOL molecules
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------
:-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx grompp -f box.mdp -c ../GLIC_pH70_popc_center_sol.pdb -p ../GLIC_pH70_popc_sol.top -o b4membed.tpr
NOTE 1 [file box.mdp, line 1]:
box.mdp did not specify a value for the .mdp option "cutoff-scheme".
Probably it was first intended for use with GROMACS before 4.6. In 4.6,
the Verlet scheme was introduced, but the group scheme was still the
default. The default is now the Verlet scheme, so you will observe
different behaviour.
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.21#
NOTE 2 [file box.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
Setting the LD random seed to -578171092
Generated 3321 of the 3321 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3321 of the 3321 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 3 [file GLIC_pH70_popc_sol.top, line 49]:
System has non-zero total charge: -29.999993
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
NOTE 4 [file GLIC_pH70_popc_sol.top, line 49]:
For energy conservation with LINCS, lincs_iter should be 2 or larger.
Cleaning up constraints and constant bonded interactions with virtual sites
Converted 2007 Bonds with virtual sites to connections, 3135 left
Removed 1602 Angles with virtual sites, 7707 left
Removed 1650 Proper Dih.s with virtual sites, 15828 left
Removing all charge groups because cutoff-scheme=Verlet
NOTE 5 [file GLIC_pH70_popc_sol.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than
10 times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group rest is 296667.00
NOTE 6 [file box.mdp]:
NVE simulation with an initial temperature of zero: will use a Verlet
buffer of 10%. Check your energy drift!
NOTE 7 [file box.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 7 notes
GROMACS reminds you: "Even if you are on the right track, you will get run over if you just sit there." (Will Rogers)
:-) GROMACS - gmx trjconv, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx trjconv, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx trjconv -f ../GLIC_pH70_popc_center_sol.pdb -o b4membed.pdb -s b4membed -ur rect -pbc mol
Will write pdb: Protein data bank file
Reading file b4membed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)
Reading file b4membed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)
Group 0 ( System) has 148243 elements
Group 1 ( Protein) has 27770 elements
Group 2 ( Protein-H) has 15030 elements
Group 3 ( C-alpha) has 1555 elements
Group 4 ( Backbone) has 4665 elements
Group 5 ( MainChain) has 6225 elements
Group 6 ( MainChain+Cb) has 7750 elements
Group 7 ( MainChain+H) has 7700 elements
Group 8 ( SideChain) has 20070 elements
Group 9 ( SideChain-H) has 8805 elements
Group 10 ( Prot-Masses) has 25370 elements
Group 11 ( non-Protein) has 120473 elements
Group 12 ( Other) has 17264 elements
Group 13 ( POPC) has 17264 elements
Group 14 ( Water) has 103209 elements
Group 15 ( SOL) has 103209 elements
Group 16 ( non-Water) has 45034 elements
Reading frame 0 time 1.000
Precision of ../GLIC_pH70_popc_center_sol.pdb is 0.0001 (nm)
'', 148243 atoms
Last frame 0 time 1.000
GROMACS reminds you: "Molecular biology is essentially the practice of biochemistry without a license." (Edwin Chargaff)
:-) GROMACS - gmx make_ndx, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx make_ndx -f ../GLIC_pH70_popc_center_sol.pdb -o index_before_gmembed.ndx
Reading structure file
Back Off! I just backed up index_before_gmembed.ndx to ./#index_before_gmembed.ndx.11#
GROMACS reminds you: "Baby, It Aint Over Till It's Over" (Lenny Kravitz)
:-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx grompp -f gmembed.mdp -c b4membed.pdb -o gmembed.tpr -maxwarn 1 -n index_before_gmembed -p ../GLIC_pH70_popc_sol.top -v
Ignoring obsolete mdp entry 'optimize-fft'
Ignoring obsolete mdp entry 'rlistlong'
Ignoring obsolete mdp entry 'nstcalclr'
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#
checking input for internal consistency...
NOTE 1 [file gmembed.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
Generated 3321 of the 3321 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3321 of the 3321 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 [file GLIC_pH70_popc_sol.top, line 49]:
System has non-zero total charge: -29.999993
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
processing coordinates...
double-checking input for internal consistency...
Calculating parameters for virtual sites
Cleaning up constraints and constant bonded interactions with virtual sites
Converted 2007 Bonds with virtual sites to connections, 3135 left
Removed 1602 Angles with virtual sites, 7707 left
Removed 1650 Proper Dih.s with virtual sites, 15828 left
renumbering atomtypes...
converting bonded parameters...
NOTE 3 [file GLIC_pH70_popc_sol.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than
10 times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
initialising group options...
processing index file...
Making dummy/rest group for Acceleration containing 148243 elements
Making dummy/rest group for Freeze containing 120473 elements
Making dummy/rest group for Energy Mon. containing 120473 elements
Making dummy/rest group for VCM containing 148243 elements
Number of degrees of freedom in T-Coupling group Protein is 0.00
Number of degrees of freedom in T-Coupling group POPC is 51791.40
Number of degrees of freedom in T-Coupling group Water is 206415.61
Making dummy/rest group for User1 containing 148243 elements
Making dummy/rest group for User2 containing 148243 elements
Making dummy/rest group for Compressed X containing 148243 elements
Making dummy/rest group for Or. Res. Fit containing 148243 elements
Making dummy/rest group for QMMM containing 148243 elements
T-Coupling has 3 element(s): Protein POPC Water
Energy Mon. has 2 element(s): Protein rest
Acceleration has 1 element(s): rest
Freeze has 2 element(s): Protein rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
Compressed X has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
WARNING 1 [file gmembed.mdp]:
Can not exclude the lattice Coulomb energy between energy groups
Checking consistency between energy and charge groups...
Estimate for the relative computational load of the PME mesh part: 0.28
writing run input file...
There were 3 notes
There was 1 warning
GROMACS reminds you: "Check Your Input" (D. Van Der Spoel)
:-) GROMACS - gmx mdrun, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx mdrun -nt 1 -s gmembed.tpr -membed gmembed.dat -c GLIC_pH70_popc_further_solvate.pdb -mn index_before_gmembed -v
Back Off! I just backed up md.log to ./#md.log.5#
Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Core(TM) i5-5257U CPU @ 2.70GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
Hardware topology: Only logical processor count
Reading file gmembed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)
Membrane embedding only supports a single rank. Choosing to use only a single thread-MPI rank.
Using 1 MPI thread
Initializing membed
Back Off! I just backed up gmembed.dat to ./#gmembed.dat.5#
Setting -cpt to -1, because embedding cannot be restarted from cpt-files.
Select a group to embed in the membrane:
Group 0 ( System) has 148243 elements
Group 1 ( Protein) has 27770 elements
Group 2 ( Protein-H) has 15030 elements
Group 3 ( C-alpha) has 1555 elements
Group 4 ( Backbone) has 4665 elements
Group 5 ( MainChain) has 6225 elements
Group 6 ( MainChain+Cb) has 7750 elements
Group 7 ( MainChain+H) has 7700 elements
Group 8 ( SideChain) has 20070 elements
Group 9 ( SideChain-H) has 8805 elements
Group 10 ( Prot-Masses) has 25370 elements
Group 11 ( non-Protein) has 120473 elements
Group 12 ( Other) has 17264 elements
Group 13 ( POPC) has 17264 elements
Group 14 ( Water) has 103209 elements
Group 15 ( SOL) has 103209 elements
Group 16 ( non-Water) has 45034 elements
Select a group:
Select a group to embed Protein into (e.g. the membrane):
Group 0 ( System) has 148243 elements
Group 1 ( Protein) has 27770 elements
Group 2 ( Protein-H) has 15030 elements
Group 3 ( C-alpha) has 1555 elements
Group 4 ( Backbone) has 4665 elements
Group 5 ( MainChain) has 6225 elements
Group 6 ( MainChain+Cb) has 7750 elements
Group 7 ( MainChain+H) has 7700 elements
Group 8 ( SideChain) has 20070 elements
Group 9 ( SideChain-H) has 8805 elements
Group 10 ( Prot-Masses) has 25370 elements
Group 11 ( non-Protein) has 120473 elements
Group 12 ( Other) has 17264 elements
Group 13 ( POPC) has 17264 elements
Group 14 ( Water) has 103209 elements
Group 15 ( SOL) has 103209 elements
Group 16 ( non-Water) has 45034 elements
Select a group: Embedding piece 0 with center of geometry: 5.243682 5.243243 6.074000
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.4#
Back Off! I just backed up traj.trr to ./#traj.trr.4#
Back Off! I just backed up ener.edr to ./#ener.edr.4#
starting mdrun 'Protein'
1000 steps, 1.0 ps.
step 900, remaining wall clock time: 16 s
Writing final coordinates.
step 1000, remaining wall clock time: 0 s
Core t (s) Wall t (s) (%)
Time: 169.175 169.175 100.0
(ns/day) (hour/ns)
Performance: 0.511 46.946
GROMACS reminds you: "It seemed a good idea at first" (Gerrit Groenhof)
:-) GROMACS - gmx solvate, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx solvate, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed
Command line:
gmx solvate -cp GLIC_pH70_popc_further_solvate.pdb -cs -o GLIC_pH70_POPC_SOL.pdb
Reading solute configuration
Protein
Containing 144818 atoms in 35573 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues
Initialising inter-atomic distances...
Warning double different entries POP C 0.45 and 0.17 on line 9 in file vdwradii.dat
Using last entry (0.45)
Generating solvent configuration
Will generate new solvent configuration of 6x6x9 boxes
Solvent box contains 189750 atoms in 63250 residues
Removed 16827 solvent atoms due to solvent-solvent overlap
Removed 158394 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 4843 residues
Generated solvent containing 14529 atoms in 4843 residues
Writing generated configuration to GLIC_pH70_POPC_SOL.pdb
Output configuration contains 159347 atoms in 40416 residues
Volume : 1758.73 (nm^3)
Density : 1057.92 (g/l)
Number of SOL molecules: 38555
GROMACS reminds you: "Should we force science down the throats of those that have no taste for it? Is it our duty to drag them kicking and screaming into the twenty-first century? I am afraid that it is." (George Porter)
Next step is to update the topology with the new number of lipids and water molecules. After that we will place ions to our system using ionic strength of 0.1M . When adding ions one can use the box volume, however membrane proteins such as GLIC contain a huge extracellular domain that cuts your solvent area by half, at least. So instead I am using molality to determine the number of ions. We also need to know the charge of the protein so that we can neutralize it. It is important that the system has a neutral charge beucase we are using an alogrithm that makes this assumption when calculation the electrostatic forces.
You would see the charge of the protein when you run pdb2gmx. But if you haven’t been paying attention to the terminal output at that step you have no idea, even if you were looking it can be overwhelming. When setting up a new system it is a good practice to examine the printed info from pdb2gmx, not just for system charge but for disulfide bridge formations, protonation states on histidines, number of chains/residues, etc. But don’t worry we won’t go back. There is a neat way of finding the total system charge with the commands below, you can use them for automating the setup later on.
[7]:
%%bash
source sources.sh
#Variables between bash magic cells are not transferable. These are not necessary when running from terminal.
SOL_NR=`grep "OW" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1}'`
LIPID_NR=`grep "POPC" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1/52}'`
#This is only needed since each bash cell starts from where you are running the notebook.
#If you are running directly from terminal you should be there already.
cd g_membed
SOL_NR2=`grep "OW" GLIC_pH70_POPC_SOL.pdb | wc | awk '{printf $1}'`
LIPID_NR2=`grep "POPC" GLIC_pH70_POPC_SOL.pdb | wc | awk '{printf $1/52}'`
cp ../GLIC_pH70_popc_sol.top GLIC_pH70_POPC_SOL.top
sed -i '' "s/$SOL_NR/$SOL_NR2/g" GLIC_pH70_POPC_SOL.top
sed -i '' "s/$LIPID_NR/$LIPID_NR2/g" GLIC_pH70_POPC_SOL.top
SYS_CHARGE=`grep qtot ../topol_Protein_chain_A.itp | tail -1 | awk '{print $11 * 5}'`
echo $SYS_CHARGE
ION_NUMBER=`echo "scale=9; (0.1 / 55.5)*$SOL_NR2" | bc `
ION_NUMBER=${ION_NUMBER%%.*}
if [ $SYS_CHARGE -gt 0 ]; then
let NEG_ION=$ION_NUMBER+$SYS_CHARGE
let POS_ION=$ION_NUMBER
echo "CL- :"$NEG_ION" Na+ :"$POS_ION
elif [ $SYS_CHARGE -lt 0 ]; then
let NEG_ION=$ION_NUMBER
let POS_ION=$ION_NUMBER-$SYS_CHARGE
echo "CL- :"$NEG_ION" Na+ :"$POS_ION
else
let NEG_ION=$ION_NUMBER
let POS_ION=$ION_NUMBER
echo "CL- :"$NEG_ION" Na+ :"$POS_ION
fi
cd ../
cp g_membed/GLIC_pH70_POPC_SOL.top GLIC_pH70_POPC_SOL_ION.top
touch ion.mdp
gmx grompp -f ion.mdp -c g_membed/GLIC_pH70_POPC_SOL.pdb -p GLIC_pH70_POPC_SOL_ION.top -o 4ion.tpr
gmx genion -s 4ion.tpr -nn $NEG_ION -np $POS_ION -p GLIC_pH70_POPC_SOL_ION.top -o GLIC_pH70_POPC_SOL_ION.pdb<<EOF
15
EOF
-30
CL- :69 Na+ :99
Analysing residue names:
There are: 1555 Protein residues
There are: 306 Other residues
There are: 38555 Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
This run will generate roughly 12 Mb of data
Will try to add 99 NA ions and 69 CL ions.
Select a continuous group of solvent molecules
Selected 15: 'SOL'
Processing topology
Replacing 168 solute molecules in topology file (GLIC_pH70_POPC_SOL_ION.top) by 99 NA and 69 CL ions.
:-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx grompp -f ion.mdp -c g_membed/GLIC_pH70_POPC_SOL.pdb -p GLIC_pH70_POPC_SOL_ION.top -o 4ion.tpr
NOTE 1 [file ion.mdp, line 1]:
ion.mdp did not specify a value for the .mdp option "cutoff-scheme".
Probably it was first intended for use with GROMACS before 4.6. In 4.6,
the Verlet scheme was introduced, but the group scheme was still the
default. The default is now the Verlet scheme, so you will observe
different behaviour.
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
NOTE 2 [file ion.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
Setting the LD random seed to 263966046
Generated 3321 of the 3321 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3321 of the 3321 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 3 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:
System has non-zero total charge: -29.999993
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
NOTE 4 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:
For energy conservation with LINCS, lincs_iter should be 2 or larger.
Cleaning up constraints and constant bonded interactions with virtual sites
Converted 2007 Bonds with virtual sites to connections, 3135 left
Removed 1602 Angles with virtual sites, 7707 left
Removed 1650 Proper Dih.s with virtual sites, 15828 left
Removing all charge groups because cutoff-scheme=Verlet
NOTE 5 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than
10 times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group rest is 317523.00
NOTE 6 [file ion.mdp]:
NVE simulation with an initial temperature of zero: will use a Verlet
buffer of 10%. Check your energy drift!
NOTE 7 [file ion.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 7 notes
Back Off! I just backed up 4ion.tpr to ./#4ion.tpr.1#
GROMACS reminds you: "You're Insignificant" (Tricky)
:-) GROMACS - gmx genion, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx genion, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx genion -s 4ion.tpr -nn 69 -np 99 -p GLIC_pH70_POPC_SOL_ION.top -o GLIC_pH70_POPC_SOL_ION.pdb
Reading file 4ion.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)
Reading file 4ion.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)
Group 0 ( System) has 159347 elements
Group 1 ( Protein) has 27770 elements
Group 2 ( Protein-H) has 15030 elements
Group 3 ( C-alpha) has 1555 elements
Group 4 ( Backbone) has 4665 elements
Group 5 ( MainChain) has 6225 elements
Group 6 ( MainChain+Cb) has 7750 elements
Group 7 ( MainChain+H) has 7700 elements
Group 8 ( SideChain) has 20070 elements
Group 9 ( SideChain-H) has 8805 elements
Group 10 ( Prot-Masses) has 25370 elements
Group 11 ( non-Protein) has 131577 elements
Group 12 ( Other) has 15912 elements
Group 13 ( POPC) has 15912 elements
Group 14 ( Water) has 115665 elements
Group 15 ( SOL) has 115665 elements
Group 16 ( non-Water) has 43682 elements
Select a group: Number of (3-atomic) solvent molecules: 38555
Back Off! I just backed up GLIC_pH70_POPC_SOL_ION.top to ./#GLIC_pH70_POPC_SOL_ION.top.1#
Using random seed 2050851929.
Replacing solvent molecule 27716 (atom 126830) with NA
Replacing solvent molecule 3783 (atom 55031) with NA
Replacing solvent molecule 19055 (atom 100847) with NA
Replacing solvent molecule 36690 (atom 153752) with NA
Replacing solvent molecule 24340 (atom 116702) with NA
Replacing solvent molecule 36564 (atom 153374) with NA
Replacing solvent molecule 13304 (atom 83594) with NA
Replacing solvent molecule 19109 (atom 101009) with NA
Replacing solvent molecule 4751 (atom 57935) with NA
Replacing solvent molecule 23314 (atom 113624) with NA
Replacing solvent molecule 22670 (atom 111692) with NA
Replacing solvent molecule 17073 (atom 94901) with NA
Replacing solvent molecule 18925 (atom 100457) with NA
Replacing solvent molecule 12974 (atom 82604) with NA
Replacing solvent molecule 17344 (atom 95714) with NA
Replacing solvent molecule 11173 (atom 77201) with NA
Replacing solvent molecule 20882 (atom 106328) with NA
Replacing solvent molecule 28435 (atom 128987) with NA
Replacing solvent molecule 8011 (atom 67715) with NA
Replacing solvent molecule 14940 (atom 88502) with NA
Replacing solvent molecule 15725 (atom 90857) with NA
Replacing solvent molecule 4113 (atom 56021) with NA
Replacing solvent molecule 30599 (atom 135479) with NA
Replacing solvent molecule 5761 (atom 60965) with NA
Replacing solvent molecule 20913 (atom 106421) with NA
Replacing solvent molecule 6678 (atom 63716) with NA
Replacing solvent molecule 3245 (atom 53417) with NA
Replacing solvent molecule 17414 (atom 95924) with NA
Replacing solvent molecule 9913 (atom 73421) with NA
Replacing solvent molecule 519 (atom 45239) with NA
Replacing solvent molecule 33326 (atom 143660) with NA
Replacing solvent molecule 5232 (atom 59378) with NA
Replacing solvent molecule 18326 (atom 98660) with NA
Replacing solvent molecule 37919 (atom 157439) with NA
Replacing solvent molecule 33850 (atom 145232) with NA
Replacing solvent molecule 37166 (atom 155180) with NA
Replacing solvent molecule 29358 (atom 131756) with NA
Replacing solvent molecule 16022 (atom 91748) with NA
Replacing solvent molecule 18996 (atom 100670) with NA
Replacing solvent molecule 30880 (atom 136322) with NA
Replacing solvent molecule 10338 (atom 74696) with NA
Replacing solvent molecule 6577 (atom 63413) with NA
Replacing solvent molecule 32372 (atom 140798) with NA
Replacing solvent molecule 32652 (atom 141638) with NA
Replacing solvent molecule 22368 (atom 110786) with NA
Replacing solvent molecule 24260 (atom 116462) with NA
Replacing solvent molecule 11572 (atom 78398) with NA
Replacing solvent molecule 35453 (atom 150041) with NA
Replacing solvent molecule 20059 (atom 103859) with NA
Replacing solvent molecule 21676 (atom 108710) with NA
Replacing solvent molecule 261 (atom 44465) with NA
Replacing solvent molecule 5908 (atom 61406) with NA
Replacing solvent molecule 2668 (atom 51686) with NA
Replacing solvent molecule 26067 (atom 121883) with NA
Replacing solvent molecule 25811 (atom 121115) with NA
Replacing solvent molecule 11519 (atom 78239) with NA
Replacing solvent molecule 17027 (atom 94763) with NA
Replacing solvent molecule 18367 (atom 98783) with NA
Replacing solvent molecule 25532 (atom 120278) with NA
Replacing solvent molecule 7259 (atom 65459) with NA
Replacing solvent molecule 18142 (atom 98108) with NA
Replacing solvent molecule 7951 (atom 67535) with NA
Replacing solvent molecule 5345 (atom 59717) with NA
Replacing solvent molecule 4550 (atom 57332) with NA
Replacing solvent molecule 28235 (atom 128387) with NA
Replacing solvent molecule 34784 (atom 148034) with NA
Replacing solvent molecule 21986 (atom 109640) with NA
Replacing solvent molecule 2852 (atom 52238) with NA
Replacing solvent molecule 35931 (atom 151475) with NA
Replacing solvent molecule 10730 (atom 75872) with NA
Replacing solvent molecule 4359 (atom 56759) with NA
Replacing solvent molecule 8419 (atom 68939) with NA
Replacing solvent molecule 20060 (atom 103862) with NA
Replacing solvent molecule 8401 (atom 68885) with NA
Replacing solvent molecule 29485 (atom 132137) with NA
Replacing solvent molecule 31688 (atom 138746) with NA
Replacing solvent molecule 37808 (atom 157106) with NA
Replacing solvent molecule 37459 (atom 156059) with NA
Replacing solvent molecule 15348 (atom 89726) with NA
Replacing solvent molecule 23148 (atom 113126) with NA
Replacing solvent molecule 27278 (atom 125516) with NA
Replacing solvent molecule 26837 (atom 124193) with NA
Replacing solvent molecule 31094 (atom 136964) with NA
Replacing solvent molecule 5749 (atom 60929) with NA
Replacing solvent molecule 4916 (atom 58430) with NA
Replacing solvent molecule 16787 (atom 94043) with NA
Replacing solvent molecule 20071 (atom 103895) with NA
Replacing solvent molecule 15802 (atom 91088) with NA
Replacing solvent molecule 32808 (atom 142106) with NA
Replacing solvent molecule 14690 (atom 87752) with NA
Replacing solvent molecule 5053 (atom 58841) with NA
Replacing solvent molecule 17352 (atom 95738) with NA
Replacing solvent molecule 31235 (atom 137387) with NA
Replacing solvent molecule 1299 (atom 47579) with NA
Replacing solvent molecule 1977 (atom 49613) with NA
Replacing solvent molecule 32139 (atom 140099) with NA
Replacing solvent molecule 13815 (atom 85127) with NA
Replacing solvent molecule 29482 (atom 132128) with NA
Replacing solvent molecule 6008 (atom 61706) with NA
Replacing solvent molecule 37367 (atom 155783) with CL
Replacing solvent molecule 20024 (atom 103754) with CL
Replacing solvent molecule 3421 (atom 53945) with CL
Replacing solvent molecule 6699 (atom 63779) with CL
Replacing solvent molecule 15764 (atom 90974) with CL
Replacing solvent molecule 3515 (atom 54227) with CL
Replacing solvent molecule 1624 (atom 48554) with CL
Replacing solvent molecule 9419 (atom 71939) with CL
Replacing solvent molecule 24896 (atom 118370) with CL
Replacing solvent molecule 12955 (atom 82547) with CL
Replacing solvent molecule 33359 (atom 143759) with CL
Replacing solvent molecule 2596 (atom 51470) with CL
Replacing solvent molecule 16448 (atom 93026) with CL
Replacing solvent molecule 15834 (atom 91184) with CL
Replacing solvent molecule 35218 (atom 149336) with CL
Replacing solvent molecule 23474 (atom 114104) with CL
Replacing solvent molecule 3118 (atom 53036) with CL
Replacing solvent molecule 37164 (atom 155174) with CL
Replacing solvent molecule 23231 (atom 113375) with CL
Replacing solvent molecule 3335 (atom 53687) with CL
Replacing solvent molecule 23269 (atom 113489) with CL
Replacing solvent molecule 15382 (atom 89828) with CL
Replacing solvent molecule 35079 (atom 148919) with CL
Replacing solvent molecule 18923 (atom 100451) with CL
Replacing solvent molecule 16693 (atom 93761) with CL
Replacing solvent molecule 7790 (atom 67052) with CL
Replacing solvent molecule 25997 (atom 121673) with CL
Replacing solvent molecule 27453 (atom 126041) with CL
Replacing solvent molecule 33171 (atom 143195) with CL
Replacing solvent molecule 37761 (atom 156965) with CL
Replacing solvent molecule 10233 (atom 74381) with CL
Replacing solvent molecule 8466 (atom 69080) with CL
Replacing solvent molecule 37623 (atom 156551) with CL
Replacing solvent molecule 34084 (atom 145934) with CL
Replacing solvent molecule 16219 (atom 92339) with CL
Replacing solvent molecule 31659 (atom 138659) with CL
Replacing solvent molecule 16188 (atom 92246) with CL
Replacing solvent molecule 36741 (atom 153905) with CL
Replacing solvent molecule 4278 (atom 56516) with CL
Replacing solvent molecule 26221 (atom 122345) with CL
Replacing solvent molecule 21019 (atom 106739) with CL
Replacing solvent molecule 18639 (atom 99599) with CL
Replacing solvent molecule 38218 (atom 158336) with CL
Replacing solvent molecule 3189 (atom 53249) with CL
Replacing solvent molecule 3487 (atom 54143) with CL
Replacing solvent molecule 10028 (atom 73766) with CL
Replacing solvent molecule 8727 (atom 69863) with CL
Replacing solvent molecule 35820 (atom 151142) with CL
Replacing solvent molecule 36283 (atom 152531) with CL
Replacing solvent molecule 2452 (atom 51038) with CL
Replacing solvent molecule 33433 (atom 143981) with CL
Replacing solvent molecule 10055 (atom 73847) with CL
Replacing solvent molecule 18177 (atom 98213) with CL
Replacing solvent molecule 11810 (atom 79112) with CL
Replacing solvent molecule 15571 (atom 90395) with CL
Replacing solvent molecule 1744 (atom 48914) with CL
Replacing solvent molecule 3339 (atom 53699) with CL
Replacing solvent molecule 9178 (atom 71216) with CL
Replacing solvent molecule 35350 (atom 149732) with CL
Replacing solvent molecule 13058 (atom 82856) with CL
Replacing solvent molecule 10457 (atom 75053) with CL
Replacing solvent molecule 3510 (atom 54212) with CL
Replacing solvent molecule 12114 (atom 80024) with CL
Replacing solvent molecule 22905 (atom 112397) with CL
Replacing solvent molecule 8956 (atom 70550) with CL
Replacing solvent molecule 23690 (atom 114752) with CL
Replacing solvent molecule 34139 (atom 146099) with CL
Replacing solvent molecule 2881 (atom 52325) with CL
Replacing solvent molecule 22449 (atom 111029) with CL
Back Off! I just backed up GLIC_pH70_POPC_SOL_ION.pdb to ./#GLIC_pH70_POPC_SOL_ION.pdb.1#
GROMACS reminds you: "If I have not seen as far as others, it is because giants were standing on my shoulders." (Hal Abelson)
Now we have a coordinate system and a topology file ready. And we are almost done with our preperations. Membrane protein systems might require a bit longer equilibration as we have a heterogeneous system. To prevent protein changing its conformation abruptly during the equilibration, we will place position restraints on all the atoms except the hydrogens. These restraints will then be gradually reduced to only backbone and the Calpha atoms of the proteins. For GMX to apply these restraints we have to create those files. Run the commands below to do just that.
[8]:
%%bash
source sources.sh
echo '; Include Position restraint file
#ifdef POSRES_HEAVY
#include "posre_Protein_chain_A.itp"
#endif
; Include Position restraint file
#ifdef POSRES_BACKBONE
#include "posre_Protein_chain_A_backbone.itp"
#endif
; Include Position restraint file
#ifdef POSRES_CA
#include "posre_Protein_chain_A_ca.itp"
#endif' >> topol_Protein_chain_A.itp
gmx make_ndx -f GLIC_pH70_POPC_SOL_ION.pdb -o posre.ndx<<EOF
keep 4
0 & chain A
0 & chain A & a CA
q
EOF
gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_backbone<<EOF
1
EOF
gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_ca<<EOF
2
EOF
cp *chain_A*itp ../run-files/
cp GLIC_pH70_POPC_SOL_ION.??? ../run-files/
cp -r amber99sb*.ff ../run-files/
Going to read 0 old index file(s)
Analysing residue names:
There are: 1555 Protein residues
There are: 306 Other residues
There are: 38387 Water residues
There are: 168 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 159011 atoms
1 Protein : 27770 atoms
2 Protein-H : 15030 atoms
3 C-alpha : 1555 atoms
4 Backbone : 4665 atoms
5 MainChain : 6225 atoms
6 MainChain+Cb : 7750 atoms
7 MainChain+H : 7700 atoms
8 SideChain : 20070 atoms
9 SideChain-H : 8805 atoms
10 Prot-Masses : 25370 atoms
11 non-Protein : 131241 atoms
12 Other : 15912 atoms
13 POPC : 15912 atoms
14 NA : 99 atoms
15 CL : 69 atoms
16 Water : 115161 atoms
17 SOL : 115161 atoms
18 non-Water : 43850 atoms
19 Ion : 168 atoms
20 POPC : 15912 atoms
21 NA : 99 atoms
22 CL : 69 atoms
23 Water_and_ions : 115329 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
>
Removed group 5 'MainChain'
Removed group 6 'MainChain+Cb'
Removed group 7 'MainChain+H'
Removed group 8 'SideChain'
Removed group 9 'SideChain-H'
Removed group 10 'Prot-Masses'
Removed group 11 'non-Protein'
Removed group 12 'Other'
Removed group 13 'POPC'
Removed group 14 'NA'
Removed group 15 'CL'
Removed group 16 'Water'
Removed group 17 'SOL'
Removed group 18 'non-Water'
Removed group 19 'Ion'
Removed group 20 'POPC'
Removed group 21 'NA'
Removed group 22 'CL'
Removed group 23 'Water_and_ions'
Removed group 0 'System'
Removed group 1 'Protein'
Removed group 2 'Protein-H'
Removed group 3 'C-alpha'
>
Copied index group 0 'Backbone'
Found 5606 atoms with chain identifier A
Merged two groups with AND: 4665 5606 -> 933
1 Backbone_&_chA : 933 atoms
>
Copied index group 0 'Backbone'
Found 5606 atoms with chain identifier A
Merged two groups with AND: 4665 5606 -> 933
Found 1555 atoms with name CA
Merged two groups with AND: 933 1555 -> 311
2 Backbone_&_chA_&_CA : 311 atoms
>
Select group to position restrain
Selected 1: 'Backbone_&_chA'
Select group to position restrain
Selected 2: 'Backbone_&_chA_&_CA'
:-) GROMACS - gmx make_ndx, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx make_ndx -f GLIC_pH70_POPC_SOL_ION.pdb -o posre.ndx
Reading structure file
Back Off! I just backed up posre.ndx to ./#posre.ndx.1#
GROMACS reminds you: "A Protein is a Set Of Coordinates" (A.P. Heiner)
:-) GROMACS - gmx genrestr, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx genrestr, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_backbone
Reading structure file
Group 0 ( Backbone) has 4665 elements
Group 1 ( Backbone_&_chA) has 933 elements
Group 2 (Backbone_&_chA_&_CA) has 311 elements
Select a group:
Back Off! I just backed up posre_Protein_chain_A_backbone.itp to ./#posre_Protein_chain_A_backbone.itp.1#
GROMACS reminds you: "Move Over Hogey Bear" (Urban Dance Squad)
:-) GROMACS - gmx genrestr, 2016.2-dev-20161028-2ed67b7 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx genrestr, version 2016.2-dev-20161028-2ed67b7
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC
Command line:
gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_ca
Reading structure file
Group 0 ( Backbone) has 4665 elements
Group 1 ( Backbone_&_chA) has 933 elements
Group 2 (Backbone_&_chA_&_CA) has 311 elements
Select a group:
Back Off! I just backed up posre_Protein_chain_A_ca.itp to ./#posre_Protein_chain_A_ca.itp.1#
GROMACS reminds you: "Art is what you can get away with." (Andy Warhol)
And we are done!