[gmx-users] dmso solvent
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 27 09:26:01 CEST 2003
On Tue, 2003-05-27 at 09:15, aswin narain wrote:
> 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.
>
then you edit the topology file yourself. It is quite easy, see chapter
5 of the manual.
> 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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--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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