In [3]:
import __main__
__main__.pymol_argv = [ 'pymol', '-cp' ]
import pymol
pymol.finish_launching()
from pymol import cmd
In [3]:
%%bash
genconf -f dppc.gro -o b_64.gro -nbox 4 4 4
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) genconf (-:
Option Filename Type Description
------------------------------------------------------------
-f dppc.gro Input Structure file: gro g96 pdb tpr etc.
-o b_64.gro Output Structure file: gro g96 pdb etc.
-trj traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-nbox vector 4 4 4 Number of boxes
-dist vector 0 0 0 Distance between boxes
-seed int 0 Random generator seed, if 0 generated from the
time
-[no]rot bool no Randomly rotate conformations
-[no]shuffle bool no Random shuffling of molecules
-[no]sort bool no Sort molecules on X coord
-block int 1 Divide the box in blocks on this number of cpus
-nmolat int 3 Number of atoms per molecule, assumed to start
from 0. If you set this wrong, it will screw up
your system!
-maxrot vector 180 180 180 Maximum random rotation
-[no]renumber bool yes Renumber residues
gcq#18: "You Should Sleep Late Man, It's Much Easier On Your Constitution" (Beastie Boys)
In [4]:
%%bash
editconf -f dppc.gro -o dppc.pdb
editconf -f b_64.gro -o b_64.pdb
Read 50 atoms Volume: 1.5477 nm^3, corresponds to roughly 600 electrons No velocities found Read 3200 atoms Volume: 99.0529 nm^3, corresponds to roughly 44500 electrons No velocities found
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) editconf (-:
Option Filename Type Description
------------------------------------------------------------
-f dppc.gro Input Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-o dppc.pdb Output, Opt! Structure file: gro g96 pdb etc.
-mead mead.pqr Output, Opt. Coordinate file for MEAD
-bf bfact.dat Input, Opt. Generic data file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]ndef bool no Choose output from default index groups
-bt enum triclinic Box type for -box and -d: triclinic, cubic,
dodecahedron or octahedron
-box vector 0 0 0 Box vector lengths (a,b,c)
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)
-d real 0 Distance between the solute and the box
-[no]c bool no Center molecule in box (implied by -box and -d)
-center vector 0 0 0 Coordinates of geometrical center
-aligncenter vector 0 0 0 Center of rotation for alignment
-align vector 0 0 0 Align to target vector
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees
-[no]princ bool no Orient molecule(s) along their principal axes
-scale vector 1 1 1 Scaling factor
-density real 1000 Density (g/L) of the output box achieved by
scaling
-[no]pbc bool no Remove the periodicity (make molecule whole again)
-resnr int -1 Renumber residues starting from resnr
-[no]grasp bool no Store the charge of the atom in the B-factor
field and the radius of the atom in the occupancy
field
-rvdw real 0.12 Default Van der Waals radius (in nm) if one can
not be found in the database or if no parameters
are present in the topology file
-[no]sig56 bool no Use rmin/2 (minimum in the Van der Waals
potential) rather than sigma/2
-[no]vdwread bool no Read the Van der Waals radii from the file
vdwradii.dat rather than computing the radii
based on the force field
-[no]atom bool no Force B-factor attachment per atom
-[no]legend bool no Make B-factor legend
-label string A Add chain label for all residues
-[no]conect bool no Add CONECT records to a .pdb file when written.
Can only be done when a topology is present
gcq#188: "Clickety Clickety Click" (System Manager From Hell)
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) editconf (-:
Option Filename Type Description
------------------------------------------------------------
-f b_64.gro Input Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-o b_64.pdb Output, Opt! Structure file: gro g96 pdb etc.
-mead mead.pqr Output, Opt. Coordinate file for MEAD
-bf bfact.dat Input, Opt. Generic data file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]ndef bool no Choose output from default index groups
-bt enum triclinic Box type for -box and -d: triclinic, cubic,
dodecahedron or octahedron
-box vector 0 0 0 Box vector lengths (a,b,c)
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)
-d real 0 Distance between the solute and the box
-[no]c bool no Center molecule in box (implied by -box and -d)
-center vector 0 0 0 Coordinates of geometrical center
-aligncenter vector 0 0 0 Center of rotation for alignment
-align vector 0 0 0 Align to target vector
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees
-[no]princ bool no Orient molecule(s) along their principal axes
-scale vector 1 1 1 Scaling factor
-density real 1000 Density (g/L) of the output box achieved by
scaling
-[no]pbc bool no Remove the periodicity (make molecule whole again)
-resnr int -1 Renumber residues starting from resnr
-[no]grasp bool no Store the charge of the atom in the B-factor
field and the radius of the atom in the occupancy
field
-rvdw real 0.12 Default Van der Waals radius (in nm) if one can
not be found in the database or if no parameters
are present in the topology file
-[no]sig56 bool no Use rmin/2 (minimum in the Van der Waals
potential) rather than sigma/2
-[no]vdwread bool no Read the Van der Waals radii from the file
vdwradii.dat rather than computing the radii
based on the force field
-[no]atom bool no Force B-factor attachment per atom
-[no]legend bool no Make B-factor legend
-label string A Add chain label for all residues
-[no]conect bool no Add CONECT records to a .pdb file when written.
Can only be done when a topology is present
gcq#188: "Clickety Clickety Click" (System Manager From Hell)
In [2]:
from IPython.display import Image
import os, sys
In [6]:
cmd.load("dppc.pdb")
cmd.ray()
In [7]:
cmd.png('pic1.png')
Out[7]:
1
In [8]:
Image(filename='pic1.png')
Out[8]:
In [4]:
cmd.load("b_64.pdb")
cmd.ray()
cmd.png("pic2.png")
Image(filename='pic2.png')
Out[4]:
In [5]:
%%bash
editconf -f b_64.gro -o b_ec -d 0.5
In [6]:
%%bash
grompp -f em -c b_ec -p b -o b_em -maxwarn 2
In [7]:
%%bash
mdrun -deffnm b_em -v
In [9]:
%%bash
genbox -cp b_em -p b -cs spc216 -o b_s
In [35]:
%%bash
grompp -f pr -c b_s -p b -o b_pr -maxwarn 1
mdrun -deffnm b_pr -v
In [36]:
%%bash
editconf -f b_s.gro -o b_s.pdb
editconf -f b_pr.gro -o b_pr.pdb
In [33]:
cmd.delete("b_pr")
cmd.delete("b_s")
cmd.load("b_s.pdb")
cmd.ray()
cmd.png("pic3.png")
Image(filename='pic3.png')
Out[33]:
In [37]:
cmd.delete("b_pr")
cmd.load("b_pr.pdb")
cmd.ray()
cmd.png("pic4.png")
Image(filename='pic4.png')
Out[37]:
In [ ]: