[gmx-users] Confusion about itp file generated by topolbuild

[Mark Abraham]

On Tue, Jun 3, 2014 at 2:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/3/14, 6:51 AM, Bikramjit Sharma wrote:
>
>> Hi all,
>> I tried to generate topology file for benzene (as a trial)  using
>> topolbuild1_3. The itp file generated is (ffben.itp in my case)
>>
>>
>> #define _FF_GAFF
>>
>> #define _FF_AMBER
>> #define _FF_USER
>>
>>
>> [ defaults ]
>> ;nbfunc     comb-rule      gen-pairs     fudgeLJ      fudgeQQ
>>    1               2               yes             0.5     0.8333
>>
>>
>> #include "ffbennb.itp"
>> #include "ffusernb.itp"
>>
>> What is the meaning of first 3 lines? Because there is no force field
>> with any of these names (appeared in those lines) in the working directory
>> and we are not assigning any path. So I am confused.
>>
>>
> Those #define statements are somewhat outdated; I don't think Gromacs uses
> them in any way.  They used to be needed in old versions, but not any more.
>

I've no idea what topolbuild intends to use them for, but through GROMACS
4.6, grompp made use of them, e.g. in interpreting $GMXLIB/top/ions.itp,
and similar files.

Mark


>> Also, following suggestions from gromacs user list (
>> https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I
>> have commented the last two lines of this itp file. So, the non bonded
>> parameter file generated by topolbuild is not used.  Is it correct?
>>
>>
> That depends on whether or not those files introduce any new parameters
> that your molecule needs.  If they do, commenting them out isn't correct.
>  If they only contain duplicate information already present in the parent
> force field, commenting them out is fine.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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