import MDAnalysis as mda
from MDAnalysis.analysis import align
from MDAnalysis.analysis.rms import rmsd
import numpy as np
nucl=mda.Universe("1kx5.pdb")
dimer=nucl.select_atoms("(segid C and resid 12:119) or (segid D and resid 26:200 )")
dimer.write("h2a_h2b_tr.pdb")
/home/armeev/miniconda3/envs/mdanalysis/lib/python3.6/site-packages/MDAnalysis/topology/guessers.py:72: UserWarning: Failed to guess the mass for the following atom types: MN warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
Performing PDB2GMX
%%bash --out out --err err
source /usr/local/gromacs/bin/GMXRC
mkdir GMX_system
cd GMX_system
ln -s ../charmm36-jul2017.ff/ .
gmx pdb2gmx -f ../h2a_h2b_tr.pdb -o init.pdb -p topol.top \
-i posre.itp -water tip3p -ff charmm36-jul2017
gmx editconf -bt cubic -d 2 -c -f init.pdb -o init_box.pdb
print('Out:\n',out)
print('Err:\n',err)
Out: turning H bonds into constraints... turning H bonds into constraints... Analysing residue names: There are: 205 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data Err: :-) GROMACS - gmx grompp, 2018.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl 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) 2001-2017, 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 2018.3 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/armeev/Projects/Modelling/MolModEdu/MDanalysis Command line: gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top -o GMX_run/minimization.tpr -r GMX_system/init_box.pdb Setting the LD random seed to -667031372 Generated 97877 of the 97903 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 64492 of the 97903 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_C' Excluding 3 bonded neighbours molecule type 'Protein_chain_D' NOTE 1 [file topol.top, line 47]: System has non-zero total charge: 21.000000 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. Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 8197.00 NOTE 2 [file Protocols/minimization.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes GROMACS reminds you: "You Look Better Upside Down" (Throwing Muses) :-) GROMACS - gmx mdrun, 2018.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl 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) 2001-2017, 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 2018.3 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/armeev/Projects/Modelling/MolModEdu/MDanalysis Command line: gmx mdrun -deffnm GMX_run/minimization Reading file GMX_run/minimization.tpr, VERSION 2018.3 (single precision) Using 1 MPI thread Using 8 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 5000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 100 in 1677 steps Potential Energy = -1.8213428e+04 Maximum force = 9.6151176e+01 on atom 2201 Norm of force = 8.3892308e+00 GROMACS reminds you: "Everybody has a plan until they get punched in the mouth" (Mike Tyson)
%%bash --out out --err err
source /usr/local/gromacs/bin/GMXRC
mkdir GMX_run
gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top \
-o GMX_run/minimization.tpr -r GMX_system/init_box.pdb
gmx mdrun -deffnm GMX_run/minimization
print('Out:\n',out)
print('Err:\n',err)
Out: turning H bonds into constraints... turning H bonds into constraints... Analysing residue names: There are: 205 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data Err: :-) GROMACS - gmx grompp, 2018.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl 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) 2001-2017, 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 2018.3 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/armeev/Projects/Modelling/MolModEdu/MDanalysis Command line: gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top -o GMX_run/minimization.tpr -r GMX_system/init_box.pdb Setting the LD random seed to -667031372 Generated 97877 of the 97903 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 64492 of the 97903 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_C' Excluding 3 bonded neighbours molecule type 'Protein_chain_D' NOTE 1 [file topol.top, line 47]: System has non-zero total charge: 21.000000 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. Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 8197.00 NOTE 2 [file Protocols/minimization.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes GROMACS reminds you: "You Look Better Upside Down" (Throwing Muses) :-) GROMACS - gmx mdrun, 2018.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl 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) 2001-2017, 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 2018.3 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/armeev/Projects/Modelling/MolModEdu/MDanalysis Command line: gmx mdrun -deffnm GMX_run/minimization Reading file GMX_run/minimization.tpr, VERSION 2018.3 (single precision) Using 1 MPI thread Using 8 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 5000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 100 in 1677 steps Potential Energy = -1.8213428e+04 Maximum force = 9.6151176e+01 on atom 2201 Norm of force = 8.3892308e+00 GROMACS reminds you: "Everybody has a plan until they get punched in the mouth" (Mike Tyson)
%%bash --out out --err err
source /usr/local/gromacs/bin/GMXRC
gmx grompp -f Protocols/equilibration_vac.mdp -c GMX_run/minimization.gro -p GMX_system/topol.top \
-o GMX_run/equilibration.tpr -r GMX_system/init_box.pdb -v
gmx mdrun -deffnm GMX_run/equilibration
print('Out:\n',out)
print('Err:\n',err)
%%bash --out out --err err
source /usr/local/gromacs/bin/GMXRC
gmx grompp -f Protocols/production_vac.mdp -c GMX_run/equilibration.gro -p GMX_system/topol.top \
-o GMX_run/production.tpr -t GMX_run/equilibration.cpt -r GMX_system/init_box.pdb -v
gmx mdrun -deffnm GMX_run/production
print('Out:\n',out)
print('Err:\n',err)