[gmx-users] [Fwd: Thanks]

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Mon Jun 16 12:27:01 CEST 2003

-------- Original Message --------
Subject: Thanks
Date: 16 Jun 2003 12:12:23 -0400
From: jiri vondrasek <jirka at uochb.cas.cz>
Organization: IOCB AS CR
To: Christoph Freudenberger <christoph.freudenberger at chemie.uni-ulm.de>

  well, PRODRG says that file PDGGMX.TOP is an .itp file. The point I am
confused totaly at most is the folllowing:
I just followed the speptide manual up to the point where grompp is
taking place
well I got the following message at the end of the program run:
my command:
grompp -v -f em -c b4em -o em -p denda1

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file gromppswhMTy
Fatal error: Found a second defaults directive, file
"/usr/local/share/gromacs/top/ffgmx.itp", line 6

sounds like you have two lines saying:
#include "ffgmx.itp"
in denda1.top and one of the .itp you are importing.
remove all references to ffgmx.itp from the .itp's.

PS: Please send your questions to the list, not to me in PM.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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