Hi GMXusers,
I am facing a problem with the latest version of the GROMACS. When I
generate the tpr file with grompp, I get the following error.
"Fatal error: moleculetype CU1+ is redefined"
The error is repeating with any molecule simulation that I try. Why is
this error caused.
Waiting for your suggessions.
#################################################################################
:-) G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
:-) 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 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.
:-) /home2/sridhar/bin/GROMACS3.3/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 1AZV_ion.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 1AZV.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1AZV_b4em.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.7#
WARNING 1 [file ../em.mdp, line unknown]:
Unknown left-hand 'define' in parameter file
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Cleaning up temporary file gromppVG7rEt
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 887
Fatal error:
moleculetype CU1+ is redefined
-------------------------------------------------------
"A Lady Shaves Her Legs" (C. Meijering)
##########################################################
begin:vcard
fn:M. Sridhar Acharya
n:Acharya;M. Sridhar
org:Centre for DNA Fingerprinting and Diagnostics;Laboratory of Computational Biology
adr:Nacharam;;ECIL Road;Hyderabad;AP;500076;INDIA
email;internet:[EMAIL PROTECTED]
title:Senior Research Fellow
tel;work:+91-(0)40-27151344
tel;home:+91-(0)40-27505833
tel;cell:+91-(0)40-9440969861
x-mozilla-html:TRUE
url:http://www.cdfd.org.in/new
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