On 8/04/2010 2:22 PM, Sepideh Soltani wrote:
Please send one email, not three. If you learn how to use your tools
properly, you make a much better impression of being someone worth
someone else's time to help.
---------- Forwarded message ----------
From: *Sepideh Soltani* <[email protected]
<mailto:[email protected]>>
Date: Wed, Apr 7, 2010 at 11:21 PM
Subject: help
To: [email protected] <mailto:[email protected]>
Hi all,
I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for
drug-enzyme complex. I did this tutorial step by step but when I used
the grompp step befor the energy minimization
"grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr"
I found the following error:
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947
Fatal error:
Atomtype CB not found
-------------------------------------------------------
Atom types are defined in the ffxxx.itp files that are #included at the
start of the .top file. Your .top and .gro no longer match, probably
because you've broken the format of the .top file. Follow the example in
chapter 5 of the manual, and read the latter parts of that chapter
thoroughly.
then I found this your answer in mailing list :
Please provide a URL. We can't tell what's a quote and what's your text
in the stuff below.
If you're using a metal ion, be prepared for problems. See
http://www.gromacs.org/Documentation/How-tos/Parameterization
Mark
The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.
and
finally I used Beta version of the PRODRG and used DRGAPH.GRO instead
of DRGFIN.GRO becase I had another problem:
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (trp_b4ion.gro, 14622)
does not match topology (trp.top, 14612)
-------------------------------------------------------
But now when again I used the grompp step befor the energy
minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o
trp_em.tpr" ) I have this problem:
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1006
Fatal error:
moleculetype CU1+ is redefined
-------------------------------------------------------
Now I don't know Is this change correct? If yes, How can I solve this
new problem.
If not How can I solve previous problem.
Thank you for your help,
Hanna
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