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

[Justin Lemkul]

On 6/4/14, 2:25 AM, Bikramjit Sharma wrote:
> 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 If  #define is outdated  then is it that gromacs does not even consider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?
>

As Mark pointed out, depending on which version of Gromacs you are using, grompp 
may need those directives to parse ions.itp or water topologies.  In the 5.0 
series, such #define statements are largely irrelevant.

> 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 .
>

I have no idea what topolbuild expects or provides.  It likely should have 
generated the nonstandard parameters and written them somewhere.

-Justin

> Regards
>
>
> 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 Those #define statements are somewhat outdated; I don't think Gromacs uses them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
>
> --
> ==================================================
>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

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

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