[gmx-users] grompp.mdp

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 27 13:34:40 CEST 2009

Hi kayal,

Well, given that it reads "Fatal error" your final question seems a
bit odd, doesn't it? How did you obtain the topology? Apparently,
there's a bit more specified in it than a single butane! Besides, I
notice that you use the GROMOS force field, which is a united atom
force field. That means that aliphatic hydrogens are collapsed onto
the bearing C atoms. Ergo, butane in a UA force field will count
exactly four atoms. But you have thirteen in your coordinate file.
Maybe it would be a good idea to read up a bit on the background of
MD: force fields, topologies, etc. Most tutorials, although commonly
aimed at proteins, will introduce these concepts and give you a feel
for the matter.


On Thu, Aug 27, 2009 at 1:20 PM, abhijit
kayal<kayalabhijitiitd at gmail.com> wrote:
> Hi,
>  I am going to analyse the normal mode analysis of n-butane. For this I
> donloaded a PDB id .Then opened in wordpad and just took the glu
> residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make
> it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created
> the topology file and did the next steps .But grompp showed the following
> error
> abhijit at SCFBioServer project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o
> ab.tp
> r
>                          :-)  G  R  O  M  A  C  S  (-:
>                       GROwing Monsters And Cloning Shrimps
>                             :-)  VERSION 4.0.4  (-:
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             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  (-:
> 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         ab.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p         ab.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o         ab.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: 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.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input
> processing
> -[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 'cpp'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Generated 380 of the 1326 non-bonded parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 2 bonded neighbours molecule type 'SOL'
> NOTE 1 [file ab.top, line 126]:
>   System has non-zero total charge: -1.000000e-00
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 4.0.4
> Source code file: grompp.c, line: 362
> Fatal error:
> number of coordinates in coordinate file (ab.gro, 13)
>              does not match topology (ab.top, 29602)
> -------------------------------------------------------
> "A Lady Shaves Her Legs" (C. Meijering)
>                               So my questioin is my way of procedding is
> wrong or right?
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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