[gmx-users] Fwd: help

[Mark Abraham]

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* <sepideh.soltani at gmail.com
> <mailto:sepideh.soltani at gmail.com>>
> Date: Wed, Apr 7, 2010 at 11:21 PM
> Subject: help
> To: gmx-users-request at gromacs.org <mailto: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
> -------------------------------------------------------

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
>