[gmx-users] dmso solvent
aswin narain
aswin_biogenie at yahoo.co.uk
Tue May 27 09:16:01 CEST 2003
I am trying to solvate 1CRL in a dmso box. But the
genbox command doesnt seem to create the appropriate
top file and as a result the grompp returns an error.
I have attached the results of both the genbox and
grommpp commands.
Could anyone help me?
Aswin
Genbox:
-------
genbox -cp c_conf.gro -cs dmso -p c.top -o c_box
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 3.1 (-:
Copyright (c) 1991-2002, University of
Groningen, The Netherlands
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 c_conf.gro Input, Opt! Generic structure:
gro g96 pdb tpr tpb tpa
-cs dmso.gro Input, Opt!, Lib. Generic
structure: gro g96 pdb tpr tpb
tpa
-ci insert.gro Input, Opt. Generic structure:
gro g96 pdb tpr tpb tpa
-o c_box.gro Output Generic structure:
gro g96 pdb
-p c.top In/Out, Opt! Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit
command line options
-nice int 19 Set the nicelevel
-box vector 0 0 0 box size
-nmol int 0 no of extra molecules to
insert
-try int 10 try inserting -nmol*-try
times
-seed int 1997 random generator seed
-vdwd real 0.105 default vdwaals distance
-shell real 0 thickness of optional
water layer around solute
Reading solute configuration
Glycine aRginine prOline Methionine Alanine Cystine
Serine
Containing 7918 atoms in 534 residues
Initialising van der waals distances...
Opening library file
/usr/local/gromacs/share/top/vdwradii.dat
Opening library file
/usr/local/gromacs/share/top/aminoacids.dat
Reading solvent configuration
"Pure DMSO, 200 ps Equilibration run at 300 K. DvdS
26/02/95"
solvent configuration contains 832 atoms in 208
residues
Initialising van der waals distances...
Will generate new solvent configuration of 4x4x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
DMSO ( 4 atoms): 9984 residues
Calculating Overlap...
box_margin = 0.48
Removed 17204 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 47854 charge groups and 47854
atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 36 x 36 x 30 cells
Succesfully made neighbourlist
nri = 59763, nrj = 1157141
Checking Protein-Solvent overlap: tested 22799 pairs,
removed 3532 atoms.
Checking Solvent-Solvent overlap: tested 62727 pairs,
removed 4252 atoms.
Added 3737 molecules
Generated solvent containing 14948 atoms in 3737
residues
Writing generated configuration to c_box.gro
Back Off! I just backed up c_box.gro to #c_box.gro#
Glycine aRginine prOline Methionine Alanine Cystine
Serine
Output configuration contains 22866 atoms in 4271
residues
WARNING: masses will be determined based on residue
and atom names,
this can deviate from the real mass of the
atom type
Opening library file
/usr/local/gromacs/share/top/atommass.dat
Volume : 571.782 (nm^3)
Density : 1013.52 (g/l)
Number of SOL molecules: 0
Processing topology
Back Off! I just backed up c.top to #c.top#
gcq#230: "Wild Pointers Couldn't Drag Me Away" (K.A.
Feenstra)
The command tail c.top returns the foll.
----------------------------------------
tail c.top
; 1 1 1000 1000 1000
; #endif
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1
Grompp
------
grompp -f em -p c.top -c c_box -o c.tpr
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili
Sauce
:-) VERSION 3.1 (-:
Copyright (c) 1991-2002, University of
Groningen, The Netherlands
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 (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file
with MD parameters
-po mdout.mdp Output grompp input file
with MD parameters
-c c_box.gro Input Generic structure:
gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Generic structure:
gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p c.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o c.tpr Output Generic run input:
tpr tpb tpa
-t traj.trr Input, Opt. Full precision
trajectory: trr trj
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit
command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first
after this time.
-np int 1 Generate statusfile for #
nodes
-[no]shuffle bool no Shuffle molecules over
nodes
-[no]sort bool no Sort molecules according
to X coordinate
-[no]rmdumbds bool yes Remove constant bonded
interactions with dummies
-load string Releative load capacity of
each node on a parallel
machine. Be sure to use
quotes around the string,
which should contain a
number for each node
-maxwarn int 10 Number of warnings after
which input processing
stops
-[no]check14 bool no Remove 1-4 interactions
without Van der Waals
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to #mdout.mdp#
Warning: as of GMX v 2.0 unit of compressibility is
truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Excluding 3 bonded neighbours for Protein 1
WARNING 1 [file "c.top", line 53269]:
System has non-zero total charge: -1.700000e+01
processing coordinates...
Fatal error: number of coordinates in coordinate file
(c_box.gro, 22866)
does not match topology (c.top, 7918)
=====
Aswin Sai Narain. S
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