[gmx-users] Re: How to add dihedral information from the GAFF topology

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 26 13:59:22 CEST 2012

On 2012-03-26 13:55, bipin singh wrote:
> Hello all,
> I am using the GAFF topology provided for octan-1-ol at Gromacs liquid
> database (http://virtualchemistry.org/molecules/111-87-5/index.php). I
> have incorporated all the parameters
> for atoms, bonds and non-bonded interaction type in the forcefield
> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top),  but I
> am not sure how to add the dihedraltypes information in ffbonded.itp
> from the GAFF topology as to add this information I need the phase and
> kd for each dihedral. Is this information is available in the GAFF
> topology provided in the Gromacs database ?

This topology is self supporting and you do not need anything else in 

You should be careful merging such parameters with an existing force 
field, because strictly speaking these are different force fields.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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