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David van der Spoel wrote:
<blockquote TYPE=CITE>On Mon, 2002-12-02 at 21:13, Ruben Martinez Buey
wrote:
<br>> Hi everybody,
<br>>
<br>> I have the next error message when run grompp:
<br>>
<br>> akilonia 35% grompp -f em.mdp -c ftsz_b4em.gro -p ftsz.top -o
<br>> ftsz_em.tpr
<br>>
:-) G R O M A C S (-:
<br>>
<br>>
Gravel Rubs Often Many Awfully Cauterized Sores
<br>>
<br>>
:-) VERSION 3.1 (-:
<br>>
<br>>
<br>> Copyright (c) 1991-2002,
University of Groningen, The Netherlands
<br>>
<br>> This program
is free software; you can redistribute it and/or
<br>> modify
it under the terms of the GNU General Public License
<br>> as published
by the Free Software Foundation; either version 2
<br>>
of the License, or (at your option) any later version.
<br>>
<br>> :-) /usr/local/gromacs/3.1_sgi/mips-sgi-irix6.5/r10000/bin/grompp
<br>> (-:
<br>>
<br>> Option Filename Type
Description
<br>> ------------------------------------------------------------
<br>> -f em.mdp
Input, Opt! grompp input file with MD parameters
<br>> -po mdout.mdp Output
grompp input file with MD parameters
<br>> -c ftsz_b4em.gro Input
Generic structure: gro g96 pdb tpr
<br>> tpb tpa
<br>> -r conf.gro
Input, Opt. Generic structure: gro g96 pdb tpr
<br>> tpb tpa
<br>> -n index.ndx Input,
Opt. Index file
<br>> -deshuf deshuf.ndx Output, Opt. Index file
<br>> -p ftsz.top
Input Topology file
<br>> -pp processed.top Output, Opt. Topology file
<br>> -o ftsz_em.tpr Output
Generic run input: tpr tpb tpa
<br>> -t traj.trr
Input, Opt. Full precision trajectory: trr trj
<br>>
<br>> Option Type
Value Description
<br>> ------------------------------------------------------
<br>> -[no]h bool
no Print help info and quit
<br>> -[no]X bool
no Use dialog box GUI to edit command line
<br>> options
<br>> -nice
int 0 Set the nicelevel
<br>> -[no]v bool
yes Be loud and noisy
<br>> -time real
-1 Take frame at or first after this time.
<br>> -np
int 1 Generate statusfile for # nodes
<br>> -[no]shuffle bool no Shuffle
molecules over nodes
<br>> -[no]sort bool
no Sort molecules according to X coordinate
<br>> -[no]rmdumbds bool yes Remove constant
bonded interactions with
<br>> dummies
<br>> -load string
Releative load capacity of each node on a
<br>> parallel
<br>>
machine. Be sure to use quotes around the
<br>> string,
<br>>
which should contain a number for each node
<br>> -maxwarn int
10 Number of warnings after which input
<br>> processing
<br>>
stops
<br>> -[no]check14 bool no Remove
1-4 interactions without Van der
<br>> Waals
<br>>
<br>> creating statusfile for 1 node...
<br>>
<br>> Back Off! I just backed up mdout.mdp to #mdout.mdp#
<br>> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
<br>> checking input for internal consistency...
<br>> calling /lib/cpp...
<br>> cpp: error /usr/local/gromacs/3.1_sgi/share/top/ff_dum.itp:1: DC_PO:
too
<br>> much pushback
<br>>
<br>strange error. Does that file include itself ?</blockquote>
<p><br><b><u>Yes, I think so!!</u></b><b><u></u></b>
<p><b><u>Groetens</u></b><b><u></u></b>
<p><b><u>Ruben</u></b>
<blockquote TYPE=CITE>
<p>>
<br>--
<br>Groeten, David.
<br>________________________________________________________________________
<br>Dr. David van der Spoel,
Biomedical center, Dept. of Biochemistry
<br>Husargatan 3, Box 576,
75123 Uppsala, Sweden
<br>phone: 46 18 471 4205
fax: 46 18 511 755
<br>spoel@xray.bmc.uu.se spoel@gromacs.org
<a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a>
<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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<pre>--
___________________________________________
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
___________________________________________</pre>
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