[gmx-users] Polarisable water

Yang Ye leafyoung81-group at yahoo.com
Sat Dec 3 14:30:21 CET 2005

The error shall be quite obvious, as shown in the output of grompp. You 
may post your topology to the list to help us know what could be wrong.

Yang Ye

Michael Bajomo wrote:

> Hi Guys,
> Sorry for being sketchy on the details. I was trying to merge an 
> unpolarised water topology file with a polarised one 
> (sw3.itp....similar to sw.itp in gromacs). I am essentially 
> repeating the Ribonuclease S -peptide tutorial in the "getting 
> started" section of the gromacs website (but with polarisable 
> water). When I preprocess the modified topology file (inorder to do 
> energy minimization...em) in grompp   *(**grompp -v -f em -c b4em -o 
> em -p speptide) *I get the following output*:*
>                   /       :-)  G  R  O  M  A  C  S  (-:
>                               S  C  A  M  O  R  G
>                              :-)  VERSION 3.3  (-:
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
> others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2004, The GROMACS development team,
>             check out / /http://www.gromacs.org/ 
> <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.
>                     :-)  /usr/local/gromacs/bin/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       b4em.gro  Input        Generic structure: gro g96 pdb tpr 
> tpb tpa
>                                    xml
>   -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr 
> tpb tpa
>                                    xml
>  -rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr 
> tpb tpa
>                                    xml
>   -n      index.ndx  Input, Opt.  Index file
> -deshuf  deshuf.ndx  Output, Opt. Index file
>   -p   speptide.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o         em.tpr  Output       Generic run input: tpr tpb tpa xml
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj
>   -e       ener.edr  Input, Opt.  Generic energy: edr ene
>       Option   Type  Value  Description
> ------------------------------------------------------
>       -[no]h   bool     no  Print help info and quit
>        -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]rmvsbds   bool    yes  Remove constant bonded interactions with 
> virtual
>                             sites
>        -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
>   -[no]renum   bool    yes  Renumber atomtypes and minimize number of
>                             atomtypes
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.81#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Cleaning up temporary file gromppaew5iO
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 754
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1/
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Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Tel: 6316-2884

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