[gmx-users] grompp error

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 24 06:34:44 CEST 2007

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_*?



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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