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

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 26 15:16:33 CEST 2012

bipin singh wrote:
> 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 David said, the topologies stand on their own.  You do not need to call any 
further information from anywhere.  The .top that you downloaded begins with a 
[defaults] directive, declares atom types, and proceeds through the rest of the 
topology with explicit parameters.

> 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.

I certainly don't see how this could have happened.  All the dihedral parameters 
are listed explicitly.  The fatal error should have printed a line number in the 
.top that is problematic, so start by investigating there.  If you have modified 
the topology in any way, then undo the changes and try again.

I did not have any trouble using this .top in an unmodified form, so I suspect 
you've altered it in some way that has broken it.


> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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