[gmx-users] Fwd: help

[Sepideh Soltani]

---------- Forwarded message ----------
From: Sepideh Soltani <sepideh.soltani at gmail.com>
Date: Wed, Apr 7, 2010 at 11:21 PM
Subject: help
To: gmx-users-request at gromacs.org


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
-------------------------------------------------------

then I found this your answer in mailing list :

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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