[gmx-users] creating topology files

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 6 01:59:57 CEST 2006

Owen, Michael wrote:
> Fellow gmx users,
> I am trying to create a topology file for TFE using the olpsaa/l force 
> field to simulate a peptide in a mixed solvent.   I created a 
> molecule.itp file (as it was suggested in the manual), a molecule.gro 
> file for TFE and I was able to place the several TFE and water molecules 
> in a box. 
> When I ran grompp before equilibrating the system, the program was 
> expecting a topology file, so I created one instead of the .itp file.  
> After trying grompp once again, I received an error message that read:

The idea is that the .itp file can be #included in multiple .top files.

> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 1180
> Fatal error:
> Incorrect number of parameters - found 4, expected 6 or 12.
> -------------------------------------------------------

This is being caused by the R-B dihedrals. (This error message should be 
improved, gromacs team.) Your [ dihedrals ] have only four parameters, 
and they need 6 (or 12 for a free-energy perturbation calculation), so 
go back and find what you did wrongly.

> My topology file is attached to this message.  I left the second 
> dihedral parameters blank since there are no planar entities in TFE, and 
> the [ pairs ] have a value of zero since the opls forcefield calculates 
> 1-4 interactions by scaling.

That sounds like asking for grompp to incorporate functions that 
evaluate to zero, rather than the pertinent defaults. I'd read the 
manual carefully, and probably eliminate these [ pairs ].


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