{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# MEMBRANE PROTEIN SIMULATION: GLIC\n", "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. \n", "\n", "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...\n", "\n", "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. \n", "\n", "#### PREREQUISITES\n", "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.\n", "\n", "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](http://www.mdtutorials.com/) are a perfect way to start.\n", "\n", "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:" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#This is a python cell, the rest of the cells are bash. Do not run this cell.\n", "#If you are on terminal use the commented out cells below for setting the environment.\n", "#export VMD=/path/to/your/vmd_executable\n", "#source /path/to/your/gmx/bin/GMXRC " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%%bash\n", "#If you are running this as a jupyter notebook run the command below to set the aliases.\n", "#You must also uncomment the lines on top of each cell\n", "#echo 'export VMD=\"/path/to/your/vmd_executable\"' >> sources.sh\n", "#echo 'source /path/to/your/gmx/bin/GMXRC' >> sources.sh\n", "echo \"export VMD=/Applications/VMD1.9.2.app/Contents/vmd/vmd_MACOSXX86\" >> sources.sh\n", "echo \"source /usr/local/gromacs/bin/GMXRC\" >> sources.sh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## PREPARE THE COORDINATES AND THE TOPOLOGY \n", "\n", "Go a head and [download the tutorial files](https://github.com/ozyo/stb_proteinart/blob/master/tutorial/GLIC/GLIC_Tutorial_gmx2016.tar.gz) 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.\n", "\n", "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. \n", "\n", "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.\n", "\n", "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. \n", "\n", "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.\n", "1. First we align the protein on its principal axes and center it at 0 0 0\n", "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.\n", "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." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {"scrolled": true}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Read 12630 atoms\n", "No velocities found\n", " system size : 11.743 8.491 11.801 (nm)\n", " center : -5.427 -1.985 -0.176 (nm)\n", " box vectors : 0.000 0.000 0.000 (nm)\n", " box angles : 0.00 0.00 0.00 (degrees)\n", " box volume : 0.00 (nm^3)\n", "\n", "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", " based on residue and atom names, since they could not be\n", " definitively assigned from the information in your input\n", " files. These guessed numbers might deviate from the mass\n", " and radius of the atom type. Please check the output\n", " files if necessary.\n", "\n", "Selected 1: 'Protein'\n", "new system size : 11.374 8.379 8.278\n", " shift : 5.426 1.985 0.173 (nm)\n", "new center : -0.000 0.000 -0.000 (nm)\n", "new box vectors : 0.000 0.000 0.000 (nm)\n", "new box angles : 0.00 0.00 0.00 (degrees)\n", "new box volume : 0.00 (nm^3)\n", "Read 12630 atoms\n", "No velocities found\n", " system size : 11.375 8.379 8.278 (nm)\n", " center : -0.000 0.000 -0.000 (nm)\n", " box vectors : 0.000 0.000 0.000 (nm)\n", " box angles : 0.00 0.00 0.00 (degrees)\n", " box volume : 0.00 (nm^3)\n", "Rotating 0, 90, 0 degrees around the X, Y and Z axis respectively\n", "new system size : 8.278 8.379 11.375\n", "new center : -0.000 0.000 0.000 (nm)\n", "Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)\n", "Info) http://www.ks.uiuc.edu/Research/vmd/ \n", "Info) Email questions and bug reports to vmd@ks.uiuc.edu \n", "Info) Please include this reference in published work using VMD: \n", "Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual \n", "Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.\n", "Info) -------------------------------------------------------------\n", "Info) Multithreading available, 4 CPUs detected.\n", "Info) Dynamically loaded 2 plugins in directory:\n", "Info) /Applications/VMD1.9.2.app/Contents/vmd/plugins/MACOSXX86/molfile\n", "The drugui package could not be loaded:\n", "\n", "/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\n", "/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\n", "Info) Using plugin pdb for structure file GLIC_princ_rotate.pdb\n", "Info) Using plugin pdb for coordinates from file GLIC_princ_rotate.pdb\n", "Info) Determining bond structure from distance search ...\n", "Info) Analyzing structure ...\n", "Info) Atoms: 12630\n", "Info) Bonds: 13192\n", "Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0\n", "Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0\n", "Info) Residues: 1555\n", "Info) Waters: 0\n", "Info) Segments: 1\n", "Info) Fragments: 5 Protein: 5 Nucleic: 0\n", "Info) Finished with coordinate file GLIC_princ_rotate.pdb.\n", "0\n", "Info) Using plugin pdb for structure file popc_332.pdb\n", "Info) Using plugin pdb for coordinates from file popc_332.pdb\n", "Info) Determining bond structure from distance search ...\n", "Info) Analyzing structure ...\n", "Info) Atoms: 77024\n", "Info) Bonds: 56772\n", "Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0\n", "Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0\n", "Info) Residues: 20252\n", "Info) Waters: 19920\n", "Info) Segments: 1\n", "Info) Fragments: 20252 Protein: 0 Nucleic: 0\n", "Info) Finished with coordinate file popc_332.pdb.\n", "1\n", "atomselect0\n", "atomselect1\n", "atomselect2\n", "51.74549865722656 52.776763916015625 45.45720672607422\n", "0.14343200623989105 0.09072847664356232 -29.331968307495117\n", "51.60206665098667 52.68603543937206 74.78917503356934\n", "51.60206665098667 52.68603543937206 74.78917503356934\n", "Info) Opened coordinate file GLIC_princ_rotate_translate.pdb for writing.\n", "Info) Finished with coordinate file GLIC_princ_rotate_translate.pdb.\n", "Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)\n", "Info) Exiting normally.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " :-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx editconf -f 4NPQ_BA1.pdb -o GLIC_princ.pdb -center 0 0 0 -princ\n", "\n", "\n", "Select group for the determining the orientation\n", "Group 0 ( System) has 12630 elements\n", "Group 1 ( Protein) has 12630 elements\n", "Group 2 ( Protein-H) has 12630 elements\n", "Group 3 ( C-alpha) has 1555 elements\n", "Group 4 ( Backbone) has 4665 elements\n", "Group 5 ( MainChain) has 6225 elements\n", "Group 6 ( MainChain+Cb) has 7750 elements\n", "Group 7 ( MainChain+H) has 6225 elements\n", "Group 8 ( SideChain) has 6405 elements\n", "Group 9 ( SideChain-H) has 6405 elements\n", "Select a group: \n", "Back Off! I just backed up GLIC_princ.pdb to ./#GLIC_princ.pdb.1#\n", "\n", "GROMACS reminds you: \"I'm Gonna Get Medieval On Your Ass\" (Pulp Fiction)\n", "\n", " :-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx editconf -f GLIC_princ.pdb -o GLIC_princ_rotate.pdb -rotate 0 90 0\n", "\n", "\n", "Back Off! I just backed up GLIC_princ_rotate.pdb to ./#GLIC_princ_rotate.pdb.1#\n", "\n", "GROMACS reminds you: \"The time for theory is over\" (J. Hajdu)\n", "\n" ] } ], "source": [ "%%bash\n", "source sources.sh\n", "\n", "gmx editconf -f 4NPQ_BA1.pdb -o GLIC_princ.pdb -center 0 0 0 -princ < GLIC_pH70_popc.pdb\n", "grep 'ATOM' GLIC_pH70.pdb >> GLIC_pH70_popc.pdb\n", "grep 'POPC' popc_332.pdb >> GLIC_pH70_popc.pdb\n", "echo 'END' >> GLIC_pH70_popc.pdb" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "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." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Read 45034 atoms\n", "Volume: 1758.73 nm^3, corresponds to roughly 791400 electrons\n", "No velocities found\n", " system size : 12.933 12.566 11.659 (nm)\n", " diameter : 16.346 (nm)\n", " center : 5.165 5.272 6.341 (nm)\n", " box vectors : 10.484 10.484 16.000 (nm)\n", " box angles : 90.00 90.00 90.00 (degrees)\n", " box volume :1758.73 (nm^3)\n", " shift : 0.077 -0.029 1.659 (nm)\n", "new center : 5.242 5.242 8.000 (nm)\n", "\n", "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", " based on residue and atom names, since they could not be\n", " definitively assigned from the information in your input\n", " files. These guessed numbers might deviate from the mass\n", " and radius of the atom type. Please check the output\n", " files if necessary.\n", "\n", "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", "from the source below. This means the results may be different\n", "compared to previous GROMACS versions.\n", "\n", "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", "A. Bondi\n", "van der Waals Volumes and Radii\n", "J. Phys. Chem. 68 (1964) pp. 441-451\n", "-------- -------- --- Thank You --- -------- --------\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " :-) GROMACS - gmx editconf, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx editconf, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx editconf -f GLIC_pH70_popc.pdb -o GLIC_pH70_popc_center.pdb -c -bt cubic\n", "\n", "\n", "Back Off! I just backed up GLIC_pH70_popc_center.pdb to ./#GLIC_pH70_popc_center.pdb.1#\n", "\n", "GROMACS reminds you: \"You Will Be Surprised At What Resides In Your Inside\" (Arrested Development)\n", "\n", " :-) GROMACS - gmx solvate, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx solvate, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx solvate -cp GLIC_pH70_popc_center.pdb -cs -o GLIC_pH70_popc_center_sol.pdb\n", "\n", "Reading solute configuration\n", "Small POP_membrane\n", "Containing 45034 atoms in 1887 residues\n", "Reading solvent configuration\n", "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984\n", "Containing 648 atoms in 216 residues\n", "\n", "Initialising inter-atomic distances...\n", "Warning double different entries POP C 0.45 and 0.17 on line 9 in file vdwradii.dat\n", "Using last entry (0.45)\n", "Generating solvent configuration\n", "Will generate new solvent configuration of 6x6x9 boxes\n", "Solvent box contains 189750 atoms in 63250 residues\n", "Removed 16827 solvent atoms due to solvent-solvent overlap\n", "Removed 69714 solvent atoms due to solute-solvent overlap\n", "Sorting configuration\n", "Found 1 molecule type:\n", " SOL ( 3 atoms): 34403 residues\n", "Generated solvent containing 103209 atoms in 34403 residues\n", "Writing generated configuration to GLIC_pH70_popc_center_sol.pdb\n", "\n", "Back Off! I just backed up GLIC_pH70_popc_center_sol.pdb to ./#GLIC_pH70_popc_center_sol.pdb.1#\n", "\n", "Output configuration contains 148243 atoms in 36290 residues\n", "Volume : 1758.73 (nm^3)\n", "Density : 1003.96 (g/l)\n", "Number of SOL molecules: 34403 \n", "\n", "\n", "GROMACS reminds you: \"I was detained, I was restrained\" (The Smiths)\n", "\n" ] } ], "source": [ "%%bash\n", "source sources.sh\n", "\n", "gmx editconf -f GLIC_pH70_popc.pdb -o GLIC_pH70_popc_center.pdb -c -bt cubic\n", "cp /usr/local/gromacs/share/gromacs/top/vdwradii.dat b_vdwradii.dat\n", "sed '/; Water charge sites/ a\\\n", "POP C 0.45 \\\n", "' b_vdwradii.dat > vdwradii.dat\n", "gmx solvate -cp GLIC_pH70_popc_center.pdb -cs -o GLIC_pH70_popc_center_sol.pdb\n", "rm vdwradii.dat" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "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.\n", "\n", "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.\n", "\n", "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." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Analysing residue names:\n", "There are: 1555 Protein residues\n", "There are: 332 Other residues\n", "There are: 34403 Water residues\n", "Analysing Protein...\n", "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "This run will generate roughly 11 Mb of data\n", "Select group for output\n", "Selected 0: 'System'\n", "Going to read 0 old index file(s)\n", "Analysing residue names:\n", "There are: 1555 Protein residues\n", "There are: 332 Other residues\n", "There are: 34403 Water residues\n", "Analysing Protein...\n", "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "\n", " 0 System : 148243 atoms\n", " 1 Protein : 27770 atoms\n", " 2 Protein-H : 15030 atoms\n", " 3 C-alpha : 1555 atoms\n", " 4 Backbone : 4665 atoms\n", " 5 MainChain : 6225 atoms\n", " 6 MainChain+Cb : 7750 atoms\n", " 7 MainChain+H : 7700 atoms\n", " 8 SideChain : 20070 atoms\n", " 9 SideChain-H : 8805 atoms\n", " 10 Prot-Masses : 25370 atoms\n", " 11 non-Protein : 120473 atoms\n", " 12 Other : 17264 atoms\n", " 13 POPC : 17264 atoms\n", " 14 Water : 103209 atoms\n", " 15 SOL : 103209 atoms\n", " 16 non-Water : 45034 atoms\n", "\n", " nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups\n", " 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues\n", " 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help\n", " 'r': residue 'res' nr 'chain' char\n", " \"name\": group 'case': case sensitive 'q': save and quit\n", " 'ri': residue index\n", "\n", "> \n", "\n", "> \n", "processing topology...\n", "Largest charge group radii for Van der Waals: 0.179, 0.169 nm\n", "Largest charge group radii for Coulomb: 0.179, 0.169 nm\n", "Calculating fourier grid dimensions for X Y Z\n", "Using a fourier grid of 96x96x144, spacing 0.109 0.109 0.111\n", "This run will generate roughly 362 Mb of data\n", "Selected 1: 'Protein'\n", "Selected 13: 'POPC'\n", "The estimated area of the protein in the membrane is 30.983 nm^2\n", "\n", "There are 281 lipids in the membrane part that overlaps the protein.\n", "The area per lipid is 0.6584 nm^2.\n", "Maximum number of lipids that will be removed is 94.\n", "\n", "Will resize the protein by a factor of 0.300 in the xy plane and 1.000 in the z direction.\n", "This resizing will be done with respect to the geometrical center of all protein atoms\n", "that span the membrane region, i.e. z between 3.240 and 8.908\n", "\n", "Will remove 0 Protein_chain_A molecules\n", "Will remove 26 POPC molecules\n", "Will remove 691 SOL molecules\n", "\n", "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", " based on residue and atom names, since they could not be\n", " definitively assigned from the information in your input\n", " files. These guessed numbers might deviate from the mass\n", " and radius of the atom type. Please check the output\n", " files if necessary.\n", "\n", "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", "from the source below. This means the results may be different\n", "compared to previous GROMACS versions.\n", "\n", "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", "A. Bondi\n", "van der Waals Volumes and Radii\n", "J. Phys. Chem. 68 (1964) pp. 441-451\n", "-------- -------- --- Thank You --- -------- --------\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " :-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx grompp -f box.mdp -c ../GLIC_pH70_popc_center_sol.pdb -p ../GLIC_pH70_popc_sol.top -o b4membed.tpr\n", "\n", "\n", "NOTE 1 [file box.mdp, line 1]:\n", " box.mdp did not specify a value for the .mdp option \"cutoff-scheme\".\n", " Probably it was first intended for use with GROMACS before 4.6. In 4.6,\n", " the Verlet scheme was introduced, but the group scheme was still the\n", " default. The default is now the Verlet scheme, so you will observe\n", " different behaviour.\n", "\n", "\n", "Back Off! I just backed up mdout.mdp to ./#mdout.mdp.21#\n", "\n", "NOTE 2 [file box.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", "\n", "Setting the LD random seed to -578171092\n", "Generated 3321 of the 3321 non-bonded parameter combinations\n", "Generating 1-4 interactions: fudge = 0.5\n", "Generated 3321 of the 3321 1-4 parameter combinations\n", "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n", "Excluding 3 bonded neighbours molecule type 'POPC'\n", "Excluding 2 bonded neighbours molecule type 'SOL'\n", "\n", "NOTE 3 [file GLIC_pH70_popc_sol.top, line 49]:\n", " System has non-zero total charge: -29.999993\n", " Total charge should normally be an integer. See\n", " http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n", " for discussion on how close it should be to an integer.\n", " \n", "\n", "\n", "\n", "NOTE 4 [file GLIC_pH70_popc_sol.top, line 49]:\n", " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", "\n", "\n", "Cleaning up constraints and constant bonded interactions with virtual sites\n", "Converted 2007 Bonds with virtual sites to connections, 3135 left\n", "Removed 1602 Angles with virtual sites, 7707 left\n", "Removed 1650 Proper Dih.s with virtual sites, 15828 left\n", "Removing all charge groups because cutoff-scheme=Verlet\n", "\n", "NOTE 5 [file GLIC_pH70_popc_sol.top, line 49]:\n", " The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG\n", " has an estimated oscillational period of 9.0e-03 ps, which is less than\n", " 10 times the time step of 1.0e-03 ps.\n", " Maybe you forgot to change the constraints mdp option.\n", "\n", "Number of degrees of freedom in T-Coupling group rest is 296667.00\n", "\n", "NOTE 6 [file box.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", "\n", "NOTE 7 [file box.mdp]:\n", " You are using a plain Coulomb cut-off, which might produce artifacts.\n", " You might want to consider using PME electrostatics.\n", "\n", "\n", "\n", "There were 7 notes\n", "\n", "GROMACS reminds you: \"Even if you are on the right track, you will get run over if you just sit there.\" (Will Rogers)\n", "\n", " :-) GROMACS - gmx trjconv, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx trjconv, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx trjconv -f ../GLIC_pH70_popc_center_sol.pdb -o b4membed.pdb -s b4membed -ur rect -pbc mol\n", "\n", "Will write pdb: Protein data bank file\n", "Reading file b4membed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)\n", "Reading file b4membed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)\n", "Group 0 ( System) has 148243 elements\n", "Group 1 ( Protein) has 27770 elements\n", "Group 2 ( Protein-H) has 15030 elements\n", "Group 3 ( C-alpha) has 1555 elements\n", "Group 4 ( Backbone) has 4665 elements\n", "Group 5 ( MainChain) has 6225 elements\n", "Group 6 ( MainChain+Cb) has 7750 elements\n", "Group 7 ( MainChain+H) has 7700 elements\n", "Group 8 ( SideChain) has 20070 elements\n", "Group 9 ( SideChain-H) has 8805 elements\n", "Group 10 ( Prot-Masses) has 25370 elements\n", "Group 11 ( non-Protein) has 120473 elements\n", "Group 12 ( Other) has 17264 elements\n", "Group 13 ( POPC) has 17264 elements\n", "Group 14 ( Water) has 103209 elements\n", "Group 15 ( SOL) has 103209 elements\n", "Group 16 ( non-Water) has 45034 elements\n", "Select a group: Reading frames from pdb file\r", "Reading frame 0 time 1.000 \n", "Precision of ../GLIC_pH70_popc_center_sol.pdb is 0.0001 (nm)\n", " -> frame 0 time 1.000 \r", " '', 148243 atoms\n", "\r", "Last frame 0 time 1.000 \n", "\n", "\n", "GROMACS reminds you: \"Molecular biology is essentially the practice of biochemistry without a license.\" (Edwin Chargaff)\n", "\n", " :-) GROMACS - gmx make_ndx, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx make_ndx, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx make_ndx -f ../GLIC_pH70_popc_center_sol.pdb -o index_before_gmembed.ndx\n", "\n", "\n", "Reading structure file\n", "\n", "Back Off! I just backed up index_before_gmembed.ndx to ./#index_before_gmembed.ndx.11#\n", "\n", "GROMACS reminds you: \"Baby, It Aint Over Till It's Over\" (Lenny Kravitz)\n", "\n", " :-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx grompp -f gmembed.mdp -c b4membed.pdb -o gmembed.tpr -maxwarn 1 -n index_before_gmembed -p ../GLIC_pH70_popc_sol.top -v\n", "\n", "Ignoring obsolete mdp entry 'optimize-fft'\n", "Ignoring obsolete mdp entry 'rlistlong'\n", "Ignoring obsolete mdp entry 'nstcalclr'\n", "Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'\n", "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", "\n", "Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#\n", "checking input for internal consistency...\n", "\n", "NOTE 1 [file gmembed.mdp]:\n", " The group cutoff scheme is deprecated since GROMACS 5.0 and will be\n", " removed in a future release when all interaction forms are supported for\n", " the verlet scheme. The verlet scheme already scales better, and it is\n", " compatible with GPUs and other accelerators.\n", "\n", "Generated 3321 of the 3321 non-bonded parameter combinations\n", "Generating 1-4 interactions: fudge = 0.5\n", "Generated 3321 of the 3321 1-4 parameter combinations\n", "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n", "Excluding 3 bonded neighbours molecule type 'POPC'\n", "Excluding 2 bonded neighbours molecule type 'SOL'\n", "\n", "NOTE 2 [file GLIC_pH70_popc_sol.top, line 49]:\n", " System has non-zero total charge: -29.999993\n", " Total charge should normally be an integer. See\n", " http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n", " for discussion on how close it should be to an integer.\n", " \n", "\n", "\n", "processing coordinates...\n", "double-checking input for internal consistency...\n", "Calculating parameters for virtual sites\n", "Cleaning up constraints and constant bonded interactions with virtual sites\n", "Converted 2007 Bonds with virtual sites to connections, 3135 left\n", "Removed 1602 Angles with virtual sites, 7707 left\n", "Removed 1650 Proper Dih.s with virtual sites, 15828 left\n", "renumbering atomtypes...\n", "converting bonded parameters...\n", "\n", "NOTE 3 [file GLIC_pH70_popc_sol.top, line 49]:\n", " The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG\n", " has an estimated oscillational period of 9.0e-03 ps, which is less than\n", " 10 times the time step of 1.0e-03 ps.\n", " Maybe you forgot to change the constraints mdp option.\n", "\n", "initialising group options...\n", "processing index file...\n", "Making dummy/rest group for Acceleration containing 148243 elements\n", "Making dummy/rest group for Freeze containing 120473 elements\n", "Making dummy/rest group for Energy Mon. containing 120473 elements\n", "Making dummy/rest group for VCM containing 148243 elements\n", "Number of degrees of freedom in T-Coupling group Protein is 0.00\n", "Number of degrees of freedom in T-Coupling group POPC is 51791.40\n", "Number of degrees of freedom in T-Coupling group Water is 206415.61\n", "Making dummy/rest group for User1 containing 148243 elements\n", "Making dummy/rest group for User2 containing 148243 elements\n", "Making dummy/rest group for Compressed X containing 148243 elements\n", "Making dummy/rest group for Or. Res. Fit containing 148243 elements\n", "Making dummy/rest group for QMMM containing 148243 elements\n", "T-Coupling has 3 element(s): Protein POPC Water\n", "Energy Mon. has 2 element(s): Protein rest\n", "Acceleration has 1 element(s): rest\n", "Freeze has 2 element(s): Protein rest\n", "User1 has 1 element(s): rest\n", "User2 has 1 element(s): rest\n", "VCM has 1 element(s): rest\n", "Compressed X has 1 element(s): rest\n", "Or. Res. Fit has 1 element(s): rest\n", "QMMM has 1 element(s): rest\n", "\n", "WARNING 1 [file gmembed.mdp]:\n", " Can not exclude the lattice Coulomb energy between energy groups\n", "\n", "Checking consistency between energy and charge groups...\n", "Estimate for the relative computational load of the PME mesh part: 0.28\n", "writing run input file...\n", "\n", "There were 3 notes\n", "\n", "There was 1 warning\n", "\n", "GROMACS reminds you: \"Check Your Input\" (D. Van Der Spoel)\n", "\n", " :-) GROMACS - gmx mdrun, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx mdrun, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx mdrun -nt 1 -s gmembed.tpr -membed gmembed.dat -c GLIC_pH70_popc_further_solvate.pdb -mn index_before_gmembed -v\n", "\n", "\n", "Back Off! I just backed up md.log to ./#md.log.5#\n", "\n", "Running on 1 node with total 4 cores, 4 logical cores\n", "Hardware detected:\n", " CPU info:\n", " Vendor: Intel\n", " Brand: Intel(R) Core(TM) i5-5257U CPU @ 2.70GHz\n", " SIMD instructions most likely to fit this hardware: AVX2_256\n", " SIMD instructions selected at GROMACS compile time: AVX2_256\n", "\n", " Hardware topology: Only logical processor count\n", "\n", "Reading file gmembed.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)\n", "\n", "Membrane embedding only supports a single rank. Choosing to use only a single thread-MPI rank.\n", "Using 1 MPI thread\n", "Initializing membed\n", "Back Off! I just backed up gmembed.dat to ./#gmembed.dat.5#\n", "\n", "Setting -cpt to -1, because embedding cannot be restarted from cpt-files.\n", "\n", "Select a group to embed in the membrane:\n", "Group 0 ( System) has 148243 elements\n", "Group 1 ( Protein) has 27770 elements\n", "Group 2 ( Protein-H) has 15030 elements\n", "Group 3 ( C-alpha) has 1555 elements\n", "Group 4 ( Backbone) has 4665 elements\n", "Group 5 ( MainChain) has 6225 elements\n", "Group 6 ( MainChain+Cb) has 7750 elements\n", "Group 7 ( MainChain+H) has 7700 elements\n", "Group 8 ( SideChain) has 20070 elements\n", "Group 9 ( SideChain-H) has 8805 elements\n", "Group 10 ( Prot-Masses) has 25370 elements\n", "Group 11 ( non-Protein) has 120473 elements\n", "Group 12 ( Other) has 17264 elements\n", "Group 13 ( POPC) has 17264 elements\n", "Group 14 ( Water) has 103209 elements\n", "Group 15 ( SOL) has 103209 elements\n", "Group 16 ( non-Water) has 45034 elements\n", "Select a group: \n", "Select a group to embed Protein into (e.g. the membrane):\n", "Group 0 ( System) has 148243 elements\n", "Group 1 ( Protein) has 27770 elements\n", "Group 2 ( Protein-H) has 15030 elements\n", "Group 3 ( C-alpha) has 1555 elements\n", "Group 4 ( Backbone) has 4665 elements\n", "Group 5 ( MainChain) has 6225 elements\n", "Group 6 ( MainChain+Cb) has 7750 elements\n", "Group 7 ( MainChain+H) has 7700 elements\n", "Group 8 ( SideChain) has 20070 elements\n", "Group 9 ( SideChain-H) has 8805 elements\n", "Group 10 ( Prot-Masses) has 25370 elements\n", "Group 11 ( non-Protein) has 120473 elements\n", "Group 12 ( Other) has 17264 elements\n", "Group 13 ( POPC) has 17264 elements\n", "Group 14 ( Water) has 103209 elements\n", "Group 15 ( SOL) has 103209 elements\n", "Group 16 ( non-Water) has 45034 elements\n", "Select a group: Embedding piece 0 with center of geometry: 5.243682 5.243243 6.074000\n", "\n", "\n", "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n", "removed in a future release when 'verlet' supports all interaction forms.\n", "\n", "\n", "Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.4#\n", "\n", "Back Off! I just backed up traj.trr to ./#traj.trr.4#\n", "\n", "Back Off! I just backed up ener.edr to ./#ener.edr.4#\n", "starting mdrun 'Protein'\n", "1000 steps, 1.0 ps.\n", "\r", "step 0\r", "step 100, remaining wall clock time: 159 s \r", "step 200, remaining wall clock time: 146 s \r", "step 300, remaining wall clock time: 124 s \r", "step 400, remaining wall clock time: 105 s \r", "step 500, remaining wall clock time: 89 s \r", "step 600, remaining wall clock time: 69 s \r", "step 700, remaining wall clock time: 51 s \r", "step 800, remaining wall clock time: 33 s \r", "step 900, remaining wall clock time: 16 s \n", "Writing final coordinates.\n", "\r", "step 1000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", " Time: 169.175 169.175 100.0\n", " (ns/day) (hour/ns)\n", "Performance: 0.511 46.946\n", "\n", "GROMACS reminds you: \"It seemed a good idea at first\" (Gerrit Groenhof)\n", "\n", " :-) GROMACS - gmx solvate, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx solvate, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC/g_membed\n", "Command line:\n", " gmx solvate -cp GLIC_pH70_popc_further_solvate.pdb -cs -o GLIC_pH70_POPC_SOL.pdb\n", "\n", "Reading solute configuration\n", "Protein\n", "Containing 144818 atoms in 35573 residues\n", "Reading solvent configuration\n", "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984\n", "Containing 648 atoms in 216 residues\n", "\n", "Initialising inter-atomic distances...\n", "Warning double different entries POP C 0.45 and 0.17 on line 9 in file vdwradii.dat\n", "Using last entry (0.45)\n", "Generating solvent configuration\n", "Will generate new solvent configuration of 6x6x9 boxes\n", "Solvent box contains 189750 atoms in 63250 residues\n", "Removed 16827 solvent atoms due to solvent-solvent overlap\n", "Removed 158394 solvent atoms due to solute-solvent overlap\n", "Sorting configuration\n", "Found 1 molecule type:\n", " SOL ( 3 atoms): 4843 residues\n", "Generated solvent containing 14529 atoms in 4843 residues\n", "Writing generated configuration to GLIC_pH70_POPC_SOL.pdb\n", "\n", "Output configuration contains 159347 atoms in 40416 residues\n", "Volume : 1758.73 (nm^3)\n", "Density : 1057.92 (g/l)\n", "Number of SOL molecules: 38555 \n", "\n", "\n", "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)\n", "\n" ] } ], "source": [ "%%bash\n", "source sources.sh\n", "\n", "SOL_NR=`grep \"OW\" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1}'`\n", "LIPID_NR=`grep \"POPC\" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1/52}'`\n", "\n", "grep -v \"Protein_chain_[B-E]\" topol.top > GLIC_pH70_popc_sol.top\n", "sed -i '' '/topol_Protein_chain_A.itp\"/ a\\\n", "#include \"amber99sb-ildn-berger.ff/popc.itp\" \\\n", "' GLIC_pH70_popc_sol.top\n", "sed -i '' 's/Protein_chain_A 1/Protein_chain_A 5/g' GLIC_pH70_popc_sol.top\n", "echo 'POPC '$LIPID_NR >> GLIC_pH70_popc_sol.top\n", "echo 'SOL '$SOL_NR >> GLIC_pH70_popc_sol.top\n", "sed -i '' 's/amber99sb-ildn.ff/amber99sb-ildn-berger.ff/g' GLIC_pH70_popc_sol.top\n", "\n", "mkdir -p g_membed\n", "cp gmembed.mdp gmembed.dat g_membed/\n", "cd g_membed\n", "rm *.tpr *.pdb\n", "touch box.mdp \n", "gmx grompp -f box.mdp -c ../GLIC_pH70_popc_center_sol.pdb -p ../GLIC_pH70_popc_sol.top -o b4membed.tpr\n", "gmx trjconv -f ../GLIC_pH70_popc_center_sol.pdb -o b4membed.pdb -s b4membed -ur rect -pbc mol< vdwradii.dat\n", "\n", "gmx solvate -cp GLIC_pH70_popc_further_solvate.pdb -cs -o GLIC_pH70_POPC_SOL.pdb\n", "rm vdwradii.dat" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "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.\n", "\n", "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." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-30\n", "CL- :69 Na+ :99\n", "Analysing residue names:\n", "There are: 1555 Protein residues\n", "There are: 306 Other residues\n", "There are: 38555 Water residues\n", "Analysing Protein...\n", "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "This run will generate roughly 12 Mb of data\n", "Will try to add 99 NA ions and 69 CL ions.\n", "Select a continuous group of solvent molecules\n", "Selected 15: 'SOL'\n", "\n", "Processing topology\n", "Replacing 168 solute molecules in topology file (GLIC_pH70_POPC_SOL_ION.top) by 99 NA and 69 CL ions.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " :-) GROMACS - gmx grompp, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx grompp, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx grompp -f ion.mdp -c g_membed/GLIC_pH70_POPC_SOL.pdb -p GLIC_pH70_POPC_SOL_ION.top -o 4ion.tpr\n", "\n", "\n", "NOTE 1 [file ion.mdp, line 1]:\n", " ion.mdp did not specify a value for the .mdp option \"cutoff-scheme\".\n", " Probably it was first intended for use with GROMACS before 4.6. In 4.6,\n", " the Verlet scheme was introduced, but the group scheme was still the\n", " default. The default is now the Verlet scheme, so you will observe\n", " different behaviour.\n", "\n", "\n", "Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#\n", "\n", "NOTE 2 [file ion.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", "\n", "Setting the LD random seed to 263966046\n", "Generated 3321 of the 3321 non-bonded parameter combinations\n", "Generating 1-4 interactions: fudge = 0.5\n", "Generated 3321 of the 3321 1-4 parameter combinations\n", "Excluding 3 bonded neighbours molecule type 'Protein_chain_A'\n", "Excluding 3 bonded neighbours molecule type 'POPC'\n", "Excluding 2 bonded neighbours molecule type 'SOL'\n", "\n", "NOTE 3 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:\n", " System has non-zero total charge: -29.999993\n", " Total charge should normally be an integer. See\n", " http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n", " for discussion on how close it should be to an integer.\n", " \n", "\n", "\n", "\n", "NOTE 4 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:\n", " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", "\n", "\n", "Cleaning up constraints and constant bonded interactions with virtual sites\n", "Converted 2007 Bonds with virtual sites to connections, 3135 left\n", "Removed 1602 Angles with virtual sites, 7707 left\n", "Removed 1650 Proper Dih.s with virtual sites, 15828 left\n", "Removing all charge groups because cutoff-scheme=Verlet\n", "\n", "NOTE 5 [file GLIC_pH70_POPC_SOL_ION.top, line 49]:\n", " The bond in molecule-type Protein_chain_A between atoms 32 OG and 33 HG\n", " has an estimated oscillational period of 9.0e-03 ps, which is less than\n", " 10 times the time step of 1.0e-03 ps.\n", " Maybe you forgot to change the constraints mdp option.\n", "\n", "Number of degrees of freedom in T-Coupling group rest is 317523.00\n", "\n", "NOTE 6 [file ion.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", "\n", "NOTE 7 [file ion.mdp]:\n", " You are using a plain Coulomb cut-off, which might produce artifacts.\n", " You might want to consider using PME electrostatics.\n", "\n", "\n", "\n", "There were 7 notes\n", "\n", "Back Off! I just backed up 4ion.tpr to ./#4ion.tpr.1#\n", "\n", "GROMACS reminds you: \"You're Insignificant\" (Tricky)\n", "\n", " :-) GROMACS - gmx genion, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx genion, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx genion -s 4ion.tpr -nn 69 -np 99 -p GLIC_pH70_POPC_SOL_ION.top -o GLIC_pH70_POPC_SOL_ION.pdb\n", "\n", "Reading file 4ion.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)\n", "Reading file 4ion.tpr, VERSION 2016.2-dev-20161028-2ed67b7 (single precision)\n", "Group 0 ( System) has 159347 elements\n", "Group 1 ( Protein) has 27770 elements\n", "Group 2 ( Protein-H) has 15030 elements\n", "Group 3 ( C-alpha) has 1555 elements\n", "Group 4 ( Backbone) has 4665 elements\n", "Group 5 ( MainChain) has 6225 elements\n", "Group 6 ( MainChain+Cb) has 7750 elements\n", "Group 7 ( MainChain+H) has 7700 elements\n", "Group 8 ( SideChain) has 20070 elements\n", "Group 9 ( SideChain-H) has 8805 elements\n", "Group 10 ( Prot-Masses) has 25370 elements\n", "Group 11 ( non-Protein) has 131577 elements\n", "Group 12 ( Other) has 15912 elements\n", "Group 13 ( POPC) has 15912 elements\n", "Group 14 ( Water) has 115665 elements\n", "Group 15 ( SOL) has 115665 elements\n", "Group 16 ( non-Water) has 43682 elements\n", "Select a group: Number of (3-atomic) solvent molecules: 38555\n", "\n", "Back Off! I just backed up GLIC_pH70_POPC_SOL_ION.top to ./#GLIC_pH70_POPC_SOL_ION.top.1#\n", "Using random seed 2050851929.\n", "Replacing solvent molecule 27716 (atom 126830) with NA\n", "Replacing solvent molecule 3783 (atom 55031) with NA\n", "Replacing solvent molecule 19055 (atom 100847) with NA\n", "Replacing solvent molecule 36690 (atom 153752) with NA\n", "Replacing solvent molecule 24340 (atom 116702) with NA\n", "Replacing solvent molecule 36564 (atom 153374) with NA\n", "Replacing solvent molecule 13304 (atom 83594) with NA\n", "Replacing solvent molecule 19109 (atom 101009) with NA\n", "Replacing solvent molecule 4751 (atom 57935) with NA\n", "Replacing solvent molecule 23314 (atom 113624) with NA\n", "Replacing solvent molecule 22670 (atom 111692) with NA\n", "Replacing solvent molecule 17073 (atom 94901) with NA\n", "Replacing solvent molecule 18925 (atom 100457) with NA\n", "Replacing solvent molecule 12974 (atom 82604) with NA\n", "Replacing solvent molecule 17344 (atom 95714) with NA\n", "Replacing solvent molecule 11173 (atom 77201) with NA\n", "Replacing solvent molecule 20882 (atom 106328) with NA\n", "Replacing solvent molecule 28435 (atom 128987) with NA\n", "Replacing solvent molecule 8011 (atom 67715) with NA\n", "Replacing solvent molecule 14940 (atom 88502) with NA\n", "Replacing solvent molecule 15725 (atom 90857) with NA\n", "Replacing solvent molecule 4113 (atom 56021) with NA\n", "Replacing solvent molecule 30599 (atom 135479) with NA\n", "Replacing solvent molecule 5761 (atom 60965) with NA\n", "Replacing solvent molecule 20913 (atom 106421) with NA\n", "Replacing solvent molecule 6678 (atom 63716) with NA\n", "Replacing solvent molecule 3245 (atom 53417) with NA\n", "Replacing solvent molecule 17414 (atom 95924) with NA\n", "Replacing solvent molecule 9913 (atom 73421) with NA\n", "Replacing solvent molecule 519 (atom 45239) with NA\n", "Replacing solvent molecule 33326 (atom 143660) with NA\n", "Replacing solvent molecule 5232 (atom 59378) with NA\n", "Replacing solvent molecule 18326 (atom 98660) with NA\n", "Replacing solvent molecule 37919 (atom 157439) with NA\n", "Replacing solvent molecule 33850 (atom 145232) with NA\n", "Replacing solvent molecule 37166 (atom 155180) with NA\n", "Replacing solvent molecule 29358 (atom 131756) with NA\n", "Replacing solvent molecule 16022 (atom 91748) with NA\n", "Replacing solvent molecule 18996 (atom 100670) with NA\n", "Replacing solvent molecule 30880 (atom 136322) with NA\n", "Replacing solvent molecule 10338 (atom 74696) with NA\n", "Replacing solvent molecule 6577 (atom 63413) with NA\n", "Replacing solvent molecule 32372 (atom 140798) with NA\n", "Replacing solvent molecule 32652 (atom 141638) with NA\n", "Replacing solvent molecule 22368 (atom 110786) with NA\n", "Replacing solvent molecule 24260 (atom 116462) with NA\n", "Replacing solvent molecule 11572 (atom 78398) with NA\n", "Replacing solvent molecule 35453 (atom 150041) with NA\n", "Replacing solvent molecule 20059 (atom 103859) with NA\n", "Replacing solvent molecule 21676 (atom 108710) with NA\n", "Replacing solvent molecule 261 (atom 44465) with NA\n", "Replacing solvent molecule 5908 (atom 61406) with NA\n", "Replacing solvent molecule 2668 (atom 51686) with NA\n", "Replacing solvent molecule 26067 (atom 121883) with NA\n", "Replacing solvent molecule 25811 (atom 121115) with NA\n", "Replacing solvent molecule 11519 (atom 78239) with NA\n", "Replacing solvent molecule 17027 (atom 94763) with NA\n", "Replacing solvent molecule 18367 (atom 98783) with NA\n", "Replacing solvent molecule 25532 (atom 120278) with NA\n", "Replacing solvent molecule 7259 (atom 65459) with NA\n", "Replacing solvent molecule 18142 (atom 98108) with NA\n", "Replacing solvent molecule 7951 (atom 67535) with NA\n", "Replacing solvent molecule 5345 (atom 59717) with NA\n", "Replacing solvent molecule 4550 (atom 57332) with NA\n", "Replacing solvent molecule 28235 (atom 128387) with NA\n", "Replacing solvent molecule 34784 (atom 148034) with NA\n", "Replacing solvent molecule 21986 (atom 109640) with NA\n", "Replacing solvent molecule 2852 (atom 52238) with NA\n", "Replacing solvent molecule 35931 (atom 151475) with NA\n", "Replacing solvent molecule 10730 (atom 75872) with NA\n", "Replacing solvent molecule 4359 (atom 56759) with NA\n", "Replacing solvent molecule 8419 (atom 68939) with NA\n", "Replacing solvent molecule 20060 (atom 103862) with NA\n", "Replacing solvent molecule 8401 (atom 68885) with NA\n", "Replacing solvent molecule 29485 (atom 132137) with NA\n", "Replacing solvent molecule 31688 (atom 138746) with NA\n", "Replacing solvent molecule 37808 (atom 157106) with NA\n", "Replacing solvent molecule 37459 (atom 156059) with NA\n", "Replacing solvent molecule 15348 (atom 89726) with NA\n", "Replacing solvent molecule 23148 (atom 113126) with NA\n", "Replacing solvent molecule 27278 (atom 125516) with NA\n", "Replacing solvent molecule 26837 (atom 124193) with NA\n", "Replacing solvent molecule 31094 (atom 136964) with NA\n", "Replacing solvent molecule 5749 (atom 60929) with NA\n", "Replacing solvent molecule 4916 (atom 58430) with NA\n", "Replacing solvent molecule 16787 (atom 94043) with NA\n", "Replacing solvent molecule 20071 (atom 103895) with NA\n", "Replacing solvent molecule 15802 (atom 91088) with NA\n", "Replacing solvent molecule 32808 (atom 142106) with NA\n", "Replacing solvent molecule 14690 (atom 87752) with NA\n", "Replacing solvent molecule 5053 (atom 58841) with NA\n", "Replacing solvent molecule 17352 (atom 95738) with NA\n", "Replacing solvent molecule 31235 (atom 137387) with NA\n", "Replacing solvent molecule 1299 (atom 47579) with NA\n", "Replacing solvent molecule 1977 (atom 49613) with NA\n", "Replacing solvent molecule 32139 (atom 140099) with NA\n", "Replacing solvent molecule 13815 (atom 85127) with NA\n", "Replacing solvent molecule 29482 (atom 132128) with NA\n", "Replacing solvent molecule 6008 (atom 61706) with NA\n", "Replacing solvent molecule 37367 (atom 155783) with CL\n", "Replacing solvent molecule 20024 (atom 103754) with CL\n", "Replacing solvent molecule 3421 (atom 53945) with CL\n", "Replacing solvent molecule 6699 (atom 63779) with CL\n", "Replacing solvent molecule 15764 (atom 90974) with CL\n", "Replacing solvent molecule 3515 (atom 54227) with CL\n", "Replacing solvent molecule 1624 (atom 48554) with CL\n", "Replacing solvent molecule 9419 (atom 71939) with CL\n", "Replacing solvent molecule 24896 (atom 118370) with CL\n", "Replacing solvent molecule 12955 (atom 82547) with CL\n", "Replacing solvent molecule 33359 (atom 143759) with CL\n", "Replacing solvent molecule 2596 (atom 51470) with CL\n", "Replacing solvent molecule 16448 (atom 93026) with CL\n", "Replacing solvent molecule 15834 (atom 91184) with CL\n", "Replacing solvent molecule 35218 (atom 149336) with CL\n", "Replacing solvent molecule 23474 (atom 114104) with CL\n", "Replacing solvent molecule 3118 (atom 53036) with CL\n", "Replacing solvent molecule 37164 (atom 155174) with CL\n", "Replacing solvent molecule 23231 (atom 113375) with CL\n", "Replacing solvent molecule 3335 (atom 53687) with CL\n", "Replacing solvent molecule 23269 (atom 113489) with CL\n", "Replacing solvent molecule 15382 (atom 89828) with CL\n", "Replacing solvent molecule 35079 (atom 148919) with CL\n", "Replacing solvent molecule 18923 (atom 100451) with CL\n", "Replacing solvent molecule 16693 (atom 93761) with CL\n", "Replacing solvent molecule 7790 (atom 67052) with CL\n", "Replacing solvent molecule 25997 (atom 121673) with CL\n", "Replacing solvent molecule 27453 (atom 126041) with CL\n", "Replacing solvent molecule 33171 (atom 143195) with CL\n", "Replacing solvent molecule 37761 (atom 156965) with CL\n", "Replacing solvent molecule 10233 (atom 74381) with CL\n", "Replacing solvent molecule 8466 (atom 69080) with CL\n", "Replacing solvent molecule 37623 (atom 156551) with CL\n", "Replacing solvent molecule 34084 (atom 145934) with CL\n", "Replacing solvent molecule 16219 (atom 92339) with CL\n", "Replacing solvent molecule 31659 (atom 138659) with CL\n", "Replacing solvent molecule 16188 (atom 92246) with CL\n", "Replacing solvent molecule 36741 (atom 153905) with CL\n", "Replacing solvent molecule 4278 (atom 56516) with CL\n", "Replacing solvent molecule 26221 (atom 122345) with CL\n", "Replacing solvent molecule 21019 (atom 106739) with CL\n", "Replacing solvent molecule 18639 (atom 99599) with CL\n", "Replacing solvent molecule 38218 (atom 158336) with CL\n", "Replacing solvent molecule 3189 (atom 53249) with CL\n", "Replacing solvent molecule 3487 (atom 54143) with CL\n", "Replacing solvent molecule 10028 (atom 73766) with CL\n", "Replacing solvent molecule 8727 (atom 69863) with CL\n", "Replacing solvent molecule 35820 (atom 151142) with CL\n", "Replacing solvent molecule 36283 (atom 152531) with CL\n", "Replacing solvent molecule 2452 (atom 51038) with CL\n", "Replacing solvent molecule 33433 (atom 143981) with CL\n", "Replacing solvent molecule 10055 (atom 73847) with CL\n", "Replacing solvent molecule 18177 (atom 98213) with CL\n", "Replacing solvent molecule 11810 (atom 79112) with CL\n", "Replacing solvent molecule 15571 (atom 90395) with CL\n", "Replacing solvent molecule 1744 (atom 48914) with CL\n", "Replacing solvent molecule 3339 (atom 53699) with CL\n", "Replacing solvent molecule 9178 (atom 71216) with CL\n", "Replacing solvent molecule 35350 (atom 149732) with CL\n", "Replacing solvent molecule 13058 (atom 82856) with CL\n", "Replacing solvent molecule 10457 (atom 75053) with CL\n", "Replacing solvent molecule 3510 (atom 54212) with CL\n", "Replacing solvent molecule 12114 (atom 80024) with CL\n", "Replacing solvent molecule 22905 (atom 112397) with CL\n", "Replacing solvent molecule 8956 (atom 70550) with CL\n", "Replacing solvent molecule 23690 (atom 114752) with CL\n", "Replacing solvent molecule 34139 (atom 146099) with CL\n", "Replacing solvent molecule 2881 (atom 52325) with CL\n", "Replacing solvent molecule 22449 (atom 111029) with CL\n", "\n", "\n", "Back Off! I just backed up GLIC_pH70_POPC_SOL_ION.pdb to ./#GLIC_pH70_POPC_SOL_ION.pdb.1#\n", "\n", "GROMACS reminds you: \"If I have not seen as far as others, it is because giants were standing on my shoulders.\" (Hal Abelson)\n", "\n" ] } ], "source": [ "%%bash\n", "source sources.sh\n", "\n", "#Variables between bash magic cells are not transferable. These are not necessary when running from terminal.\n", "SOL_NR=`grep \"OW\" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1}'`\n", "LIPID_NR=`grep \"POPC\" GLIC_pH70_popc_center_sol.pdb | wc | awk '{printf $1/52}'`\n", "\n", "#This is only needed since each bash cell starts from where you are running the notebook. \n", "#If you are running directly from terminal you should be there already.\n", "cd g_membed\n", "\n", "SOL_NR2=`grep \"OW\" GLIC_pH70_POPC_SOL.pdb | wc | awk '{printf $1}'`\n", "LIPID_NR2=`grep \"POPC\" GLIC_pH70_POPC_SOL.pdb | wc | awk '{printf $1/52}'`\n", "\n", "cp ../GLIC_pH70_popc_sol.top GLIC_pH70_POPC_SOL.top\n", "sed -i '' \"s/$SOL_NR/$SOL_NR2/g\" GLIC_pH70_POPC_SOL.top\n", "sed -i '' \"s/$LIPID_NR/$LIPID_NR2/g\" GLIC_pH70_POPC_SOL.top\n", "\n", "SYS_CHARGE=`grep qtot ../topol_Protein_chain_A.itp | tail -1 | awk '{print $11 * 5}'`\n", "\n", "echo $SYS_CHARGE\n", "ION_NUMBER=`echo \"scale=9; (0.1 / 55.5)*$SOL_NR2\" | bc `\n", "ION_NUMBER=${ION_NUMBER%%.*}\n", "\n", "if [ $SYS_CHARGE -gt 0 ]; then\n", " let NEG_ION=$ION_NUMBER+$SYS_CHARGE\n", " let POS_ION=$ION_NUMBER\n", " echo \"CL- :\"$NEG_ION\" Na+ :\"$POS_ION\n", "elif [ $SYS_CHARGE -lt 0 ]; then\n", " let NEG_ION=$ION_NUMBER\n", " let POS_ION=$ION_NUMBER-$SYS_CHARGE\n", " echo \"CL- :\"$NEG_ION\" Na+ :\"$POS_ION\n", "else\n", " let NEG_ION=$ION_NUMBER\n", " let POS_ION=$ION_NUMBER\n", " echo \"CL- :\"$NEG_ION\" Na+ :\"$POS_ION\n", "fi\n", "\n", "cd ../\n", "cp g_membed/GLIC_pH70_POPC_SOL.top GLIC_pH70_POPC_SOL_ION.top\n", "touch ion.mdp\n", "gmx grompp -f ion.mdp -c g_membed/GLIC_pH70_POPC_SOL.pdb -p GLIC_pH70_POPC_SOL_ION.top -o 4ion.tpr\n", "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< \n", "Removed group 5 'MainChain'\n", "Removed group 6 'MainChain+Cb'\n", "Removed group 7 'MainChain+H'\n", "Removed group 8 'SideChain'\n", "Removed group 9 'SideChain-H'\n", "Removed group 10 'Prot-Masses'\n", "Removed group 11 'non-Protein'\n", "Removed group 12 'Other'\n", "Removed group 13 'POPC'\n", "Removed group 14 'NA'\n", "Removed group 15 'CL'\n", "Removed group 16 'Water'\n", "Removed group 17 'SOL'\n", "Removed group 18 'non-Water'\n", "Removed group 19 'Ion'\n", "Removed group 20 'POPC'\n", "Removed group 21 'NA'\n", "Removed group 22 'CL'\n", "Removed group 23 'Water_and_ions'\n", "Removed group 0 'System'\n", "Removed group 1 'Protein'\n", "Removed group 2 'Protein-H'\n", "Removed group 3 'C-alpha'\n", "\n", "> \n", "Copied index group 0 'Backbone'\n", "Found 5606 atoms with chain identifier A\n", "Merged two groups with AND: 4665 5606 -> 933\n", "\n", " 1 Backbone_&_chA : 933 atoms\n", "\n", "> \n", "Copied index group 0 'Backbone'\n", "Found 5606 atoms with chain identifier A\n", "Merged two groups with AND: 4665 5606 -> 933\n", "Found 1555 atoms with name CA\n", "Merged two groups with AND: 933 1555 -> 311\n", "\n", " 2 Backbone_&_chA_&_CA : 311 atoms\n", "\n", "> \n", "Select group to position restrain\n", "Selected 1: 'Backbone_&_chA'\n", "Select group to position restrain\n", "Selected 2: 'Backbone_&_chA_&_CA'\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " :-) GROMACS - gmx make_ndx, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx make_ndx, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx make_ndx -f GLIC_pH70_POPC_SOL_ION.pdb -o posre.ndx\n", "\n", "\n", "Reading structure file\n", "\n", "Back Off! I just backed up posre.ndx to ./#posre.ndx.1#\n", "\n", "GROMACS reminds you: \"A Protein is a Set Of Coordinates\" (A.P. Heiner)\n", "\n", " :-) GROMACS - gmx genrestr, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx genrestr, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_backbone\n", "\n", "\n", "Reading structure file\n", "Group 0 ( Backbone) has 4665 elements\n", "Group 1 ( Backbone_&_chA) has 933 elements\n", "Group 2 (Backbone_&_chA_&_CA) has 311 elements\n", "Select a group: \n", "Back Off! I just backed up posre_Protein_chain_A_backbone.itp to ./#posre_Protein_chain_A_backbone.itp.1#\n", "\n", "GROMACS reminds you: \"Move Over Hogey Bear\" (Urban Dance Squad)\n", "\n", " :-) GROMACS - gmx genrestr, 2016.2-dev-20161028-2ed67b7 (-:\n", "\n", " GROMACS is written by:\n", " Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar \n", " Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof \n", " Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis\n", " Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson \n", " Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund \n", " Teemu Murtola Szilard Pall Sander Pronk Roland Schulz \n", " Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman \n", " Teemu Virolainen Christian Wennberg Maarten Wolf \n", " and the project leaders:\n", " Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n", "\n", "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n", "Copyright (c) 2001-2015, The GROMACS development team at\n", "Uppsala University, Stockholm University and\n", "the Royal Institute of Technology, Sweden.\n", "check out http://www.gromacs.org for more information.\n", "\n", "GROMACS is free software; you can redistribute it and/or modify it\n", "under the terms of the GNU Lesser General Public License\n", "as published by the Free Software Foundation; either version 2.1\n", "of the License, or (at your option) any later version.\n", "\n", "GROMACS: gmx genrestr, version 2016.2-dev-20161028-2ed67b7\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /Users/cattibrie_fr/Documents/stb_proteinart/tutorial/GLIC\n", "Command line:\n", " gmx genrestr -f GLIC_pH70_POPC_SOL_ION.pdb -n posre.ndx -o posre_Protein_chain_A_ca\n", "\n", "\n", "Reading structure file\n", "Group 0 ( Backbone) has 4665 elements\n", "Group 1 ( Backbone_&_chA) has 933 elements\n", "Group 2 (Backbone_&_chA_&_CA) has 311 elements\n", "Select a group: \n", "Back Off! I just backed up posre_Protein_chain_A_ca.itp to ./#posre_Protein_chain_A_ca.itp.1#\n", "\n", "GROMACS reminds you: \"Art is what you can get away with.\" (Andy Warhol)\n", "\n" ] } ], "source": [ "%%bash\n", "source sources.sh\n", "\n", "echo '; Include Position restraint file\n", "#ifdef POSRES_HEAVY\n", "#include \"posre_Protein_chain_A.itp\"\n", "#endif\n", " \n", "; Include Position restraint file\n", "#ifdef POSRES_BACKBONE\n", "#include \"posre_Protein_chain_A_backbone.itp\"\n", "#endif\n", " \n", "; Include Position restraint file \n", "#ifdef POSRES_CA\n", "#include \"posre_Protein_chain_A_ca.itp\"\n", "#endif' >> topol_Protein_chain_A.itp\n", "\n", "gmx make_ndx -f GLIC_pH70_POPC_SOL_ION.pdb -o posre.ndx<