[gmx-users] creating topology files

Owen, Michael MichaelOwen at creighton.edu
Thu Oct 5 18:08:25 CEST 2006

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:

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.

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.

Could you suggest any changes to my topology file?

Thank you in advance,

Michael Owen

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