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

bipin singh bipinelmat at gmail.com
Mon Mar 26 15:05:50 CEST 2012

Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there anyway (Possibility
of using Standalone GAFF parameters in Gromacs) to do it without
performing this task.

As you said these topologies are self supporting and we do not need to
change ffbonded.itp, but during grompp I got the following error, may
be because I have not added the dihedral information.

ERROR [file oct.top]:
  No default Proper Dih. types

Please provide your suggestions.

On Mon, Mar 26, 2012 at 17:29, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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
> ffbonded.itp.
> 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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Bipin Singh

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