[gmx-users] (no subject)

[Ruben Martinez Buey]

David van der Spoel wrote:

> On Mon, 2002-12-02 at 21:13, Ruben Martinez Buey wrote:
> > Hi everybody,
> >
> > I have the next error message when run grompp:
> >
> > akilonia 35% grompp -f em.mdp -c ftsz_b4em.gro -p ftsz.top -o
> > ftsz_em.tpr
> >                          :-)  G  R  O  M  A  C  S  (-:
> >
> >                 Gravel Rubs Often Many Awfully Cauterized Sores
> >
> >                              :-)  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.
> >
> >     :-)  /usr/local/gromacs/3.1_sgi/mips-sgi-irix6.5/r10000/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  ftsz_b4em.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       ftsz.top  Input         Topology file
> >  -pp  processed.top  Output, Opt.  Topology file
> >   -o    ftsz_em.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...
> > cpp: error /usr/local/gromacs/3.1_sgi/share/top/ff_dum.itp:1: DC_PO: too
> > much pushback
> >
> strange error. Does that file include itself ?

Yes, I think so!!

Groetens

Ruben

>
>
> >
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,          75123 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20021203/b3bc6656/attachment.html>