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

[bipin singh]

Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried grompp on this
biphasic system (containing octane+water+protein), it results in error
even if I include the topologies in forcefield.itp file.

The error was

Fatal error:
Atomtype hc not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>
>>
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
-----------------------
Regards,
Bipin Singh