Ссылка на практикум.
In [29]:
from IPython.display import Image
import os, sys
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd
from IPython.display import Image
Моделирование перехода ДНК из А в В форму¶
Координаты дуплекса с последовательностью GATCTA:
In [11]:
%%bash
wget http://kodomo.cmm.msu.ru/~golovin/nucl_melt/dna.pdb
--2016-04-07 16:33:48-- http://kodomo.cmm.msu.ru/~golovin/nucl_melt/dna.pdb
Resolving kodomo.cmm.msu.ru... 93.180.63.127
Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 13608 (13K) [chemical/x-pdb]
Saving to: `dna.pdb'
0K .......... ... 100% 607M=0s
2016-04-07 16:33:48 (607 MB/s) - `dna.pdb' saved [13608/13608]
In [22]:
cmd.reinitialize()
cmd.load('dna.pdb')
cmd.show_as('cartoon')
cmd.rotate(axis='x', angle=90)
cmd.ray()
cmd.png('dna.png')
Image(filename='dna.png')
Out[22]:
Подредактируем дуплекс:
In [12]:
f = open('dna.pdb', 'r')
a = f.read()
f.close()
a = a.replace('C5M', 'C7 ')
a = a.replace('''ATOM 1 P G A 1 3.063 8.025 -4.135\nATOM 2 O1P G A 1 3.223 8.856 -5.350\nATOM 3 O2P G A 1 1.891 7.121 -4.118\n''', '')
a = a.replace('''ATOM 124 P T B 7 -5.216 6.825 -8.605\nATOM 125 O1P T B 7 -5.606 7.576 -7.390\nATOM 126 O2P T B 7 -3.836 6.291 -8.622\n''', '')
for x in ['A', 'G', 'T', 'C']:
a = a.replace(' {} '.format(x), ' D{} '.format(x))
g = open('dna.pdb', 'w')
g.write(a)
g.close()
Файл параметров для минимизации энергии:
In [3]:
%%bash
wget http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/em.mdp
--2016-04-07 15:55:51-- http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/em.mdp
Resolving kodomo.cmm.msu.ru... 93.180.63.127
Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1089 (1.1K)
Saving to: `em.mdp'
0K . 100% 142M=0s
2016-04-07 15:55:51 (142 MB/s) - `em.mdp' saved [1089/1089]
Файл параметров для "утряски" воды:
In [4]:
%%bash
wget http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/pr.mdp
--2016-04-07 15:56:21-- http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/pr.mdp
Resolving kodomo.cmm.msu.ru... 93.180.63.127
Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1180 (1.2K)
Saving to: `pr.mdp'
0K . 100% 116M=0s
2016-04-07 15:56:21 (116 MB/s) - `pr.mdp' saved [1180/1180]
Файл параметров для молекулярной динамики:
In [5]:
%%bash
wget http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/md.mdp
--2016-04-07 15:57:05-- http://kodomo.cmm.msu.ru/~golovin/nucl_a2b/md.mdp
Resolving kodomo.cmm.msu.ru... 93.180.63.127
Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1165 (1.1K)
Saving to: `md.mdp'
0K . 100% 111M=0s
2016-04-07 15:57:05 (111 MB/s) - `md.mdp' saved [1165/1165]
Теперь построим файл топологии системы в силовом поле amber99sb и файл с координатами в формате Gromacs:
In [13]:
%%bash
pdb2gmx -f dna.pdb -o dna -p dna -ff amber99sb -water tip3p
Using the Amber99sb force field in directory amber99sb.ff Reading dna.pdb... Read 240 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 12 residues with 240 atoms chain #res #atoms 1 'A' 6 120 2 'B' 6 120 Reading residue database... (amber99sb) Processing chain 1 'A' (120 atoms, 6 residues) Identified residue DG1 as a starting terminus. Identified residue DA6 as a ending terminus. Checking for duplicate atoms.... Now there are 6 residues with 190 atoms Chain time... Processing chain 2 'B' (120 atoms, 6 residues) Identified residue DT7 as a starting terminus. Identified residue DC12 as a ending terminus. Checking for duplicate atoms.... Now there are 6 residues with 190 atoms Chain time... Including chain 1 in system: 190 atoms 6 residues Including chain 2 in system: 190 atoms 6 residues --------- PLEASE NOTE ------------ You have successfully generated a topology from: dna.pdb. The Amber99sb force field and the tip3p water model are used. --------- ETON ESAELP ------------ gcq#95: "Sort Of" (Urban Dance Squad)
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) 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.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f dna.pdb Input Structure file: gro g96 pdb tpr etc.
-o dna.gro Output Structure file: gro g96 pdb etc.
-p dna.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.
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
-chainsep enum id_or_ter Condition in PDB files when a new chain should
be started (adding termini): id_or_ter,
id_and_ter, ter, id or interactive
-merge enum no Merge multiple chains into a single
[moleculetype]: no, all or interactive
-ff string amber99sb Force field, interactive by default. Use -h
for information.
-water enum tip3p Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, instead of charged
(default)
-[no]lys bool no Interactive lysine selection, instead of charged
-[no]arg bool no Interactive arginine selection, instead of charged
-[no]asp bool no Interactive aspartic acid selection, instead of
charged
-[no]glu bool no Interactive glutamic acid selection, instead of
charged
-[no]gln bool no Interactive glutamine selection, instead of
neutral
-[no]his bool no Interactive histidine selection, instead of
checking H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
phenylalanine, tryptophane and tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the coordinate
file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no Renumber the residues consecutively in the output
-[no]rtpres bool no Use .rtp entry names as residue names
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.r2b
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/amber99sb.ff/atomtypes.atp
Atomtype 1
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
Back Off! I just backed up dna.top to ./#dna.top.3#
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.arn
Making bonds...
Number of bonds was 204, now 204
Generating angles, dihedrals and pairs...
Before cleaning: 493 pairs
Before cleaning: 538 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 538 dihedrals, 34 impropers, 369 angles
475 pairs, 204 bonds and 0 virtual sites
Total mass 1786.220 a.m.u.
Total charge -5.000 e
Writing topology
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.arn
Making bonds...
Number of bonds was 204, now 204
Generating angles, dihedrals and pairs...
Before cleaning: 493 pairs
Before cleaning: 538 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 538 dihedrals, 34 impropers, 369 angles
475 pairs, 204 bonds and 0 virtual sites
Total mass 1786.220 a.m.u.
Total charge -5.000 e
Writing topology
Now there are 380 atoms and 12 residues
Total mass in system 3572.440 a.m.u.
Total charge in system -10.000 e
Writing coordinate file...
Сделаем небольшой отступ в ячейке от ДНК:
In [14]:
%%bash
editconf -f dna.gro -o dna_ec -d 1.5
Read 380 atoms
Volume: 9.81811 nm^3, corresponds to roughly 4400 electrons
No velocities found
system size : 2.092 1.906 2.462 (nm)
center : 0.055 -0.324 -0.638 (nm)
box vectors : 2.093 1.906 2.461 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 9.82 (nm^3)
shift : 2.491 2.777 3.369 (nm)
new center : 2.546 2.453 2.731 (nm)
new box vectors : 5.092 4.906 5.462 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 136.45 (nm^3)
WARNING: No boxtype specified - distance condition applied in each dimension.
If the molecule rotates the actual distance will be smaller. You might want
to use a cubic box instead, or why not try a dodecahedron today?
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) 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 dna.gro Input Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-o dna_ec.gro 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 1.5 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#145: "I Solve Problems" (Pulp Fiction)
Проведём оптимизацию геометрии системы, что бы удалить "плохие" контакты в молекуле:
In [15]:
%%bash
grompp -f em -c dna_ec -p dna -o dna_em -maxwarn 1
mdrun -deffnm dna_em -v
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) 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.
:-) grompp (-:
Analysing residue names:
There are: 12 DNA residues
This run will generate roughly 78 Mb of data
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c dna_ec.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p dna.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o dna_em.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy 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]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
WARNING 1 [file em.mdp]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
NOTE 1 [file dna.top, line 45]:
System has non-zero total charge: -9.999999
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.
Number of degrees of freedom in T-Coupling group rest is 1137.00
NOTE 2 [file em.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
There was 1 warning
gcq#352: "What's the point, yo, what's the spread?" (Red Hot Chili Peppers)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) 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.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s dna_em.tpr Input Run input file: tpr tpb tpa
-o dna_em.trr Output Full precision trajectory: trr trj cpt
-x dna_em.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi dna_em.cpt Input, Opt. Checkpoint file
-cpo dna_em.cpt Output, Opt. Checkpoint file
-c dna_em.gro Output Structure file: gro g96 pdb etc.
-e dna_em.edr Output Energy file
-g dna_em.log Output Log file
-dhdl dna_em.xvg Output, Opt. xvgr/xmgr file
-field dna_em.xvg Output, Opt. xvgr/xmgr file
-table dna_em.xvg Input, Opt. xvgr/xmgr file
-tablep dna_em.xvg Input, Opt. xvgr/xmgr file
-tableb dna_em.xvg Input, Opt. xvgr/xmgr file
-rerun dna_em.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi dna_em.xvg Output, Opt. xvgr/xmgr file
-tpid dna_em.xvg Output, Opt. xvgr/xmgr file
-ei dna_em.edi Input, Opt. ED sampling input
-eo dna_em.edo Output, Opt. ED sampling output
-j dna_em.gct Input, Opt. General coupling stuff
-jo dna_em.gct Output, Opt. General coupling stuff
-ffout dna_em.xvg Output, Opt. xvgr/xmgr file
-devout dna_em.xvg Output, Opt. xvgr/xmgr file
-runav dna_em.xvg Output, Opt. xvgr/xmgr file
-px dna_em.xvg Output, Opt. xvgr/xmgr file
-pf dna_em.xvg Output, Opt. xvgr/xmgr file
-mtx dna_em.mtx Output, Opt. Hessian matrix
-dn dna_em.ndx Output, Opt. Index file
-multidir dna_em Input, Opt., Mult. Run directory
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
-deffnm string dna_em Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file dna_em.tpr, VERSION 4.5.5 (single precision)
The integration or electrostatics algorithm doesn't support parallel runs. Not starting any threads.
Loaded with Money
Low-Memory BFGS Minimizer:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 1000000
Using 10 BFGS correction steps.
F-max = 4.11919e+03 on atom 68
F-Norm = 2.16189e+03
Step 0, Epot=-2.693403e+03, Fnorm=1.938e+03, Fmax=4.684e+03 (atom 12)
Step 1, Epot=-3.267604e+03, Fnorm=5.966e+02, Fmax=1.375e+03 (atom 345)
Step 2, Epot=-3.331010e+03, Fnorm=4.160e+02, Fmax=1.297e+03 (atom 345)
Step 3, Epot=-3.453115e+03, Fnorm=4.455e+02, Fmax=1.107e+03 (atom 109)
Step 4, Epot=-3.548926e+03, Fnorm=4.913e+02, Fmax=1.678e+03 (atom 209)
Step 5, Epot=-3.677977e+03, Fnorm=3.762e+02, Fmax=1.132e+03 (atom 118)
Step 6, Epot=-3.765992e+03, Fnorm=2.522e+02, Fmax=8.161e+02 (atom 304)
Step 7, Epot=-4.190927e+03, Fnorm=2.381e+02, Fmax=8.972e+02 (atom 209)
Step 8, Epot=-3.860009e+03, Fnorm=2.070e+02, Fmax=1.176e+03 (atom 304)
Step 9, Epot=-4.325879e+03, Fnorm=2.715e+02, Fmax=1.754e+03 (atom 50)
Step 10, Epot=-4.343688e+03, Fnorm=2.072e+02, Fmax=1.149e+03 (atom 50)
Step 11, Epot=-4.308836e+03, Fnorm=1.898e+02, Fmax=1.322e+03 (atom 50)
Step 12, Epot=-4.685551e+03, Fnorm=2.143e+02, Fmax=9.032e+02 (atom 117)
Step 13, Epot=-4.230444e+03, Fnorm=2.353e+02, Fmax=1.541e+03 (atom 239)
Step 14, Epot=-4.568479e+03, Fnorm=1.562e+02, Fmax=1.135e+03 (atom 239)
Step 15, Epot=-4.127753e+03, Fnorm=1.722e+02, Fmax=8.950e+02 (atom 176)
Step 16, Epot=-3.903042e+03, Fnorm=1.521e+02, Fmax=6.798e+02 (atom 304)
Step 17, Epot=-4.104794e+03, Fnorm=2.069e+02, Fmax=1.400e+03 (atom 239)
Step 18, Epot=-4.228642e+03, Fnorm=1.814e+02, Fmax=1.539e+03 (atom 176)
Step 19, Epot=-4.478969e+03, Fnorm=1.432e+02, Fmax=6.353e+02 (atom 238)
Step 20, Epot=-4.561273e+03, Fnorm=1.496e+02, Fmax=9.287e+02 (atom 176)
Step 21, Epot=-4.628560e+03, Fnorm=1.513e+02, Fmax=1.166e+03 (atom 176)
Step 22, Epot=-4.954081e+03, Fnorm=1.551e+02, Fmax=8.487e+02 (atom 303)
Step 23, Epot=-4.115771e+03, Fnorm=1.337e+02, Fmax=6.497e+02 (atom 114)
Step 24, Epot=-4.628033e+03, Fnorm=1.463e+02, Fmax=7.681e+02 (atom 50)
Step 25, Epot=-4.542325e+03, Fnorm=1.447e+02, Fmax=8.691e+02 (atom 50)
Step 26, Epot=-3.484835e+03, Fnorm=1.548e+02, Fmax=8.384e+02 (atom 176)
Step 27, Epot=-3.834961e+03, Fnorm=1.496e+02, Fmax=7.799e+02 (atom 338)
Step 28, Epot=-4.029127e+03, Fnorm=1.459e+02, Fmax=7.528e+02 (atom 176)
Step 29, Epot=-3.396496e+03, Fnorm=1.913e+02, Fmax=1.398e+03 (atom 50)
Step 30, Epot=-3.724763e+03, Fnorm=1.580e+02, Fmax=8.015e+02 (atom 118)
Step 31, Epot=-3.848414e+03, Fnorm=1.538e+02, Fmax=8.613e+02 (atom 176)
Step 32, Epot=-4.300494e+03, Fnorm=1.669e+02, Fmax=1.102e+03 (atom 239)
Step 33, Epot=-4.030838e+03, Fnorm=1.642e+02, Fmax=6.055e+02 (atom 367)
Step 34, Epot=-4.366114e+03, Fnorm=1.565e+02, Fmax=6.624e+02 (atom 117)
Step 35, Epot=-4.654558e+03, Fnorm=2.003e+02, Fmax=1.133e+03 (atom 85)
Step 36, Epot=-4.218182e+03, Fnorm=1.438e+02, Fmax=6.041e+02 (atom 239)
Step 37, Epot=-4.572850e+03, Fnorm=1.370e+02, Fmax=8.941e+02 (atom 239)
Step 38, Epot=-3.981932e+03, Fnorm=1.271e+02, Fmax=5.522e+02 (atom 239)
Step 39, Epot=-4.675414e+03, Fnorm=1.613e+02, Fmax=8.324e+02 (atom 239)
Step 40, Epot=-4.335334e+03, Fnorm=1.432e+02, Fmax=5.640e+02 (atom 303)
Step 41, Epot=-4.297029e+03, Fnorm=1.541e+02, Fmax=9.719e+02 (atom 146)
Step 42, Epot=-3.762649e+03, Fnorm=1.783e+02, Fmax=1.107e+03 (atom 338)
Step 43, Epot=-3.968099e+03, Fnorm=1.933e+02, Fmax=1.270e+03 (atom 304)
Step 44, Epot=-4.381287e+03, Fnorm=1.576e+02, Fmax=7.481e+02 (atom 239)
Step 45, Epot=-4.629731e+03, Fnorm=1.376e+02, Fmax=7.744e+02 (atom 21)
Step 46, Epot=-4.411564e+03, Fnorm=1.223e+02, Fmax=6.567e+02 (atom 239)
Step 47, Epot=-4.878684e+03, Fnorm=1.709e+02, Fmax=8.517e+02 (atom 239)
Step 48, Epot=-5.127947e+03, Fnorm=1.464e+02, Fmax=7.756e+02 (atom 239)
Step 49, Epot=-4.653473e+03, Fnorm=1.760e+02, Fmax=1.052e+03 (atom 113)
Step 50, Epot=-4.897924e+03, Fnorm=1.479e+02, Fmax=7.957e+02 (atom 113)
Step 51, Epot=-5.726213e+03, Fnorm=1.512e+02, Fmax=7.758e+02 (atom 368)
Step 52, Epot=-4.856182e+03, Fnorm=1.511e+02, Fmax=8.993e+02 (atom 304)
Step 53, Epot=-4.689688e+03, Fnorm=1.647e+02, Fmax=1.032e+03 (atom 368)
Step 54, Epot=-4.983457e+03, Fnorm=1.697e+02, Fmax=9.435e+02 (atom 304)
Step 55, Epot=-5.246723e+03, Fnorm=1.696e+02, Fmax=1.178e+03 (atom 21)
Step 56, Epot=-5.038355e+03, Fnorm=1.729e+02, Fmax=8.258e+02 (atom 275)
Step 57, Epot=-5.417827e+03, Fnorm=1.463e+02, Fmax=6.879e+02 (atom 338)
Step 58, Epot=-5.485213e+03, Fnorm=1.414e+02, Fmax=9.662e+02 (atom 275)
Step 59, Epot=-5.246881e+03, Fnorm=1.556e+02, Fmax=8.101e+02 (atom 239)
Step 60, Epot=-5.080242e+03, Fnorm=1.560e+02, Fmax=1.008e+03 (atom 21)
Step 61, Epot=-5.400743e+03, Fnorm=1.500e+02, Fmax=8.987e+02 (atom 304)
Step 62, Epot=-6.130639e+03, Fnorm=1.746e+02, Fmax=1.297e+03 (atom 21)
Step 63, Epot=-6.073590e+03, Fnorm=1.496e+02, Fmax=1.171e+03 (atom 21)
Step 65, Epot=-5.572796e+03, Fnorm=1.135e+02, Fmax=7.206e+02 (atom 275)
Step 66, Epot=-5.364112e+03, Fnorm=1.139e+02, Fmax=9.270e+02 (atom 239)
Step 68, Epot=-5.817999e+03, Fnorm=3.801e+02, Fmax=3.272e+03 (atom 176)
Step 69, Epot=-5.829086e+03, Fnorm=2.648e+02, Fmax=2.192e+03 (atom 176)
Step 70, Epot=-5.205772e+03, Fnorm=2.712e+02, Fmax=2.358e+03 (atom 176)
Step 71, Epot=-5.607863e+03, Fnorm=2.715e+02, Fmax=2.610e+03 (atom 176)
Step 72, Epot=-5.095579e+03, Fnorm=1.850e+02, Fmax=1.337e+03 (atom 21)
Step 73, Epot=-5.009247e+03, Fnorm=1.326e+02, Fmax=8.909e+02 (atom 50)
Step 74, Epot=-6.134985e+03, Fnorm=1.216e+02, Fmax=6.854e+02 (atom 304)
Step 75, Epot=-5.426882e+03, Fnorm=1.410e+02, Fmax=8.180e+02 (atom 176)
Step 76, Epot=-4.979729e+03, Fnorm=1.399e+02, Fmax=7.734e+02 (atom 176)
Step 77, Epot=-4.918803e+03, Fnorm=1.567e+02, Fmax=1.313e+03 (atom 304)
Step 78, Epot=-5.713594e+03, Fnorm=1.596e+02, Fmax=1.005e+03 (atom 239)
Step 79, Epot=-5.682230e+03, Fnorm=1.442e+02, Fmax=9.580e+02 (atom 176)
Step 80, Epot=-5.835149e+03, Fnorm=2.063e+02, Fmax=1.341e+03 (atom 304)
Step 81, Epot=-5.054111e+03, Fnorm=1.654e+02, Fmax=1.039e+03 (atom 304)
Step 82, Epot=-5.842374e+03, Fnorm=2.242e+02, Fmax=1.680e+03 (atom 304)
Step 83, Epot=-6.171062e+03, Fnorm=1.165e+02, Fmax=6.801e+02 (atom 176)
Step 84, Epot=-5.624493e+03, Fnorm=1.064e+02, Fmax=7.188e+02 (atom 239)
Step 85, Epot=-4.741758e+03, Fnorm=1.092e+02, Fmax=8.163e+02 (atom 176)
Step 86, Epot=-4.969585e+03, Fnorm=1.266e+02, Fmax=8.172e+02 (atom 50)
Step 87, Epot=-5.768093e+03, Fnorm=1.223e+02, Fmax=8.529e+02 (atom 239)
Step 88, Epot=-6.232039e+03, Fnorm=1.384e+02, Fmax=1.026e+03 (atom 275)
Step 89, Epot=-6.073851e+03, Fnorm=1.338e+02, Fmax=8.447e+02 (atom 275)
Step 91, Epot=-6.114540e+03, Fnorm=1.335e+02, Fmax=1.012e+03 (atom 239)
Step 92, Epot=-6.187414e+03, Fnorm=1.215e+02, Fmax=9.836e+02 (atom 239)
Step 93, Epot=-6.034576e+03, Fnorm=1.004e+02, Fmax=7.389e+02 (atom 176)
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Low-Memory BFGS Minimizer converged to machine precision in 94 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -6.0345762e+03
Maximum force = 7.3891937e+02 on atom 176
Norm of force = 1.1061332e+02
gcq#101: "My Heart is Just a Muscle In a Cavity" (F. Black)
В ходе оптимизации была уменьшена максимальная сила c Fmax=4.684e+03 (действовала на атом 12) до Fmax=7.389e+02 (действует на атом 176).
Добавим в ячейку молекулы воды:
In [16]:
%%bash
genbox -cp dna_em -p dna -cs -o dna_s
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Grid: 12 x 12 x 13 cells
Adding line for 4319 solvent molecules to topology file (dna.top)
:-) 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.
:-) genbox (-:
Option Filename Type Description
------------------------------------------------------------
-cp dna_em.gro Input, Opt! Structure file: gro g96 pdb tpr etc.
-cs spc216.gro Input, Opt!, Lib. Structure file: gro g96 pdb tpr etc.
-ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-o dna_s.gro Output Structure file: gro g96 pdb etc.
-p dna.top In/Out, Opt! Topology 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 19 Set the nicelevel
-box vector 0 0 0 Box size
-nmol int 0 Number of extra molecules to insert
-try int 10 Try inserting -nmol times -try times
-seed int 1997 Random generator seed
-vdwd real 0.105 Default van der Waals distance
-shell real 0 Thickness of optional water layer around solute
-maxsol int 0 Maximum number of solvent molecules to add if
they fit in the box. If zero (default) this is
ignored
-[no]vel bool no Keep velocities from input solute and solvent
Reading solute configuration
Protein
Containing 380 atoms in 12 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 3x3x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 5832 residues
Calculating Overlap...
box_margin = 0.315
Removed 1872 atoms that were outside the box
Successfully made neighbourlist
nri = 26808, nrj = 497850
Checking Protein-Solvent overlap: tested 6809 pairs, removed 471 atoms.
Checking Solvent-Solvent overlap: tested 156036 pairs, removed 2196 atoms.
Added 4319 molecules
Generated solvent containing 12957 atoms in 4319 residues
Writing generated configuration to dna_s.gro
Protein
Output configuration contains 13337 atoms in 4331 residues
Volume : 136.448 (nm^3)
Density : 990.925 (g/l)
Number of SOL molecules: 4319
Processing topology
Back Off! I just backed up dna.top to ./#dna.top.4#
gcq#192: "It's So Fast It's Slow" (F. Black)
Нейтрализуем заряд системы. Это делаем в два шага: строим tpr и запускаем genion
In [21]:
%%bash
grompp -f em -p dna -c dna_s -o dna_s -maxwarn 2
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) 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.
:-) grompp (-:
Analysing residue names:
There are: 12 DNA residues
There are: 4319 Water residues
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb: 0.084, 0.084 nm
This run will generate roughly 1859 Mb of data
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c dna_s.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p dna.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o dna_s.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy 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]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 2 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
WARNING 1 [file em.mdp]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file dna.top, line 46]:
System has non-zero total charge: -9.999999
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.
Number of degrees of freedom in T-Coupling group rest is 27051.00
NOTE 2 [file em.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
There was 1 warning
gcq#78: "It Costs Too Much If It Costs a Lot" (Magnapop)
In [22]:
%%bash
#из консоли, указывая группу №3
genion -s dna_s -o dna_si -p dna -np 10
Will try to add 10 NA ions and 0 CL ions. Select a continuous group of solvent molecules
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) 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.
:-) genion (-:
Option Filename Type Description
------------------------------------------------------------
-s dna_s.tpr Input Run input file: tpr tpb tpa
-table table.xvg Input, Opt. xvgr/xmgr file
-n index.ndx Input, Opt. Index file
-o dna_si.gro Output Structure file: gro g96 pdb etc.
-g genion.log Output Log file
-pot pot.pdb Output, Opt. Protein data bank file
-p dna.top In/Out, Opt! Topology 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 19 Set the nicelevel
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-np int 10 Number of positive ions
-pname string NA Name of the positive ion
-pq int 1 Charge of the positive ion
-nn int 0 Number of negative ions
-nname string CL Name of the negative ion
-nq int -1 Charge of the negative ion
-rmin real 0.6 Minimum distance between ions
-[no]random bool yes Use random placement of ions instead of based on
potential. The rmin option should still work
-seed int 1993 Seed for random number generator
-scale real 0.001 Scaling factor for the potential for -pot
-conc real 0 Specify salt concentration (mol/liter). This will
add sufficient ions to reach up to the specified
concentration as computed from the volume of the
cell in the input .tpr file. Overrides the -np
and -nn options.
-[no]neutral bool no This option will add enough ions to neutralize
the system. In combination with the concentration
option a neutral system at a given salt
concentration will be generated.
Back Off! I just backed up genion.log to ./#genion.log.1#
Reading file dna_s.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 0.35 nm
Group 0 ( System) has 13337 elements
Group 1 ( DNA) has 380 elements
Group 2 ( Water) has 12957 elements
Group 3 ( SOL) has 12957 elements
Group 4 ( non-Water) has 380 elements
Select a group:
-------------------------------------------------------
Program genion, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/index.c, line: 1036
Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Hangout In the Suburbs If You've Got the Guts" (Urban Dance Squad)
Проведём "утряску" воды:
In [23]:
%%bash
grompp -f pr -c dna_si -p dna -o dna_pr -maxwarn 1
mdrun -deffnm dna_pr -v
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) 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.
:-) grompp (-:
turning all bonds into constraints...
turning all bonds into constraints...
turning all bonds into constraints...
turning all bonds into constraints...
Analysing residue names:
There are: 12 DNA residues
There are: 4309 Water residues
There are: 10 Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb: 0.084, 0.084 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 45x42x48, spacing 0.113 0.117 0.114
This run will generate roughly 2 Mb of data
Option Filename Type Description
------------------------------------------------------------
-f pr.mdp Input grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c dna_si.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p dna.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o dna_pr.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy 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]v bool no Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 1 Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
NOTE 1 [file pr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group DNA is 731.92
Number of degrees of freedom in T-Coupling group SOL is 25851.09
Number of degrees of freedom in T-Coupling group NA is 30.00
Estimate for the relative computational load of the PME mesh part: 0.29
There was 1 note
gcq#178: "Ramones For Ever" (P.J. Van Maaren)
:-) G R O M A C S (-:
S C A M O R G
:-) 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.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s dna_pr.tpr Input Run input file: tpr tpb tpa
-o dna_pr.trr Output Full precision trajectory: trr trj cpt
-x dna_pr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi dna_pr.cpt Input, Opt. Checkpoint file
-cpo dna_pr.cpt Output, Opt. Checkpoint file
-c dna_pr.gro Output Structure file: gro g96 pdb etc.
-e dna_pr.edr Output Energy file
-g dna_pr.log Output Log file
-dhdl dna_pr.xvg Output, Opt. xvgr/xmgr file
-field dna_pr.xvg Output, Opt. xvgr/xmgr file
-table dna_pr.xvg Input, Opt. xvgr/xmgr file
-tablep dna_pr.xvg Input, Opt. xvgr/xmgr file
-tableb dna_pr.xvg Input, Opt. xvgr/xmgr file
-rerun dna_pr.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi dna_pr.xvg Output, Opt. xvgr/xmgr file
-tpid dna_pr.xvg Output, Opt. xvgr/xmgr file
-ei dna_pr.edi Input, Opt. ED sampling input
-eo dna_pr.edo Output, Opt. ED sampling output
-j dna_pr.gct Input, Opt. General coupling stuff
-jo dna_pr.gct Output, Opt. General coupling stuff
-ffout dna_pr.xvg Output, Opt. xvgr/xmgr file
-devout dna_pr.xvg Output, Opt. xvgr/xmgr file
-runav dna_pr.xvg Output, Opt. xvgr/xmgr file
-px dna_pr.xvg Output, Opt. xvgr/xmgr file
-pf dna_pr.xvg Output, Opt. xvgr/xmgr file
-mtx dna_pr.mtx Output, Opt. Hessian matrix
-dn dna_pr.ndx Output, Opt. Index file
-multidir dna_pr Input, Opt., Mult. Run directory
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
-deffnm string dna_pr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 0 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file dna_pr.tpr, VERSION 4.5.5 (single precision)
Starting 8 threads
Loaded with Money
Making 2D domain decomposition 4 x 2 x 1
starting mdrun 'Protein in water'
1000 steps, 0.2 ps.
step 900, remaining runtime: 2 s imb F 16%
Writing final coordinates.
step 1000, remaining runtime: 0 s
Average load imbalance: 17.9 %
Part of the total run time spent waiting due to load imbalance: 2.1 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 26.684 26.684 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 101.403 5.851 0.648 37.023
gcq#355: "I Like You. I Will Kill You Last" (Tyler in Fishtank)
Переформатируем dna_pr.gro и dna_si.gro в pdb формат:
In [25]:
%%bash
editconf -f dna_pr.gro -o dna_pr.pdb
editconf -f dna_si.gro -o dna_si.pdb
Read 13317 atoms Volume: 136.448 nm^3, corresponds to roughly 61400 electrons Velocities found Read 13317 atoms Volume: 136.448 nm^3, corresponds to roughly 61400 electrons No velocities found
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) 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 dna_pr.gro Input Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-o dna_pr.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
Back Off! I just backed up dna_pr.pdb to ./#dna_pr.pdb.1#
gcq#198: "Just Give Me a Blip" (F. Black)
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) 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 dna_si.gro Input Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-o dna_si.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#313: "California, R.I.P." (Red Hot Chili Peppars)
In [27]:
%%bash
pymol dna_*.pdb
PyMOL(TM) Molecular Graphics System, Version 1.5.0.1.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce 210/PCIe/SSE2
GL_VERSION: 1.4 (2.1.2 NVIDIA 340.32)
Detected 8 CPU cores. Enabled multithreaded rendering.
CmdLoad: "dna.pdb" loaded as "dna".
TITLE Protein in water
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 1 symmetry operators.
CmdLoad: "dna_pr.pdb" loaded as "dna_pr".
TITLE Protein in water
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 1 symmetry operators.
CmdLoad: "dna_si.pdb" loaded as "dna_si".
ScenePNG: wrote 640x480 pixel image to file "/home/students/y12/popov/public_html/term8/Task7/before.png".
ScenePNG: wrote 640x480 pixel image to file "/home/students/y12/popov/public_html/term8/Task7/after.png".
PyMOL: normal program termination.
libGL error: failed to load driver: swrast
In [30]:
Image(filename='before.png')
Out[30]:
In [32]:
Image(filename='after.png')
Out[32]:
Видно, что до утряски молекулы воды были выстроены регулярно, как в кристалле (видно в левом верхнем углу).
Скопируем всё на суперкомпьютер:
In []:
%%bash
scp -r ./* skif:_scratch/fbb/popov/
In []:
job 1272853