[gmx-users] grompp error

[Triguero, Luciano O]

Hi Tsjerk

Thanks a lot for your suggestions. They help me to find and solve my error.
 
Cheers,
 
Luciano
 
Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
 

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Tue 4/24/2007 12:34 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] grompp error



Hi Luciano,

Look in the topology file where your metal complex is defined (under
each [ ] section, but this seems to me to be a dihedral). You've not
given enough parameters for one of the bonded definitions.
Furthermore, it is likely that the error is in the .rtp entry,
assuming you generated one. Maybe you gave a gb_* definition where it
should have been a gd_*?

Cheers,

Tsjerk

On 4/23/07, Triguero, Luciano O <ltriguero at miami.edu> wrote:
> Hi Everybody,
>
> I have been working with the topolgy file creating a new residue type to include some metal-aminoacids ligand complex.
> So far, pdb2gmx provide the topology file without errors and this file seems to contain all te interaction I added in the correspondign databases. However, the grompp gives the following error message after processing the (.top) file.
> Any sugestion where to look or solve this problem?
>
> Thank is advance,
>
> Luciano
>
> =======================Error message follows ===============================================
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 272 of the 1711 non-bonded parameter combinations
> Cleaning up temporary file gromppq3nMBs
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 1180
> Fatal error:
> Incorrect number of parameters - found 2, expected 3 or 6.
> -------------------------------------------------------
> ===============================================================================
>
>
> Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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