[gmx-users] Re: How to add dihedral information from the GAFF topology
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 26 23:50:07 CEST 2012
bipin singh wrote:
> 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
If you introduce a new atomtype in your topology somewhere (presumably in one of
the GAFF topologies), then you have to declare them in an [atomtypes] directive
in the appropriate place in the .top file. These types are case sensitive as
well. For dealing with GAFF-type topologies, assuming you can #include them
within whatever AMBER force field you've chosen (up to you to prove), you can do
[ moleculetype ]
The inclusion of the ligand topology (at this specific location) will add the
new [atomtypes] at the appropriate level of precedence, before any
[moleculetypes] are declared.
> 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.
>>> On Mon, Mar 26, 2012 at 17:29, David van der Spoel <spoel at xray.bmc.uu.se>
>>>> 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
>>>> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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