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

Bikramjit Sharma bikramjit_101 at yahoo.com
Wed Jun 4 08:25:14 CEST 2014

Thanks for your reply Justin, but my confusion in the first part is not being removed. If  #define is outdated  then is it that gromacs does not even consider those lines? Then how does gromacs use those force fields during grompp? 

Also, if somehow gormacs considers those force fields then where is the location of them. There is no force field with such names   in the working directory, neither in topolbuild directory nor in gromacs top directory .  


On Tuesday, June 3, 2014 6:05 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Those #define statements are somewhat outdated; I don't think Gromacs uses them 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.

> 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 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


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