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

[Justin A. Lemkul]

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 
something like:

#include "amberXX.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]
;name       nrexcl
Protein     3

(etc)

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.

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================