[gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 20 15:33:22 CET 2011



Qin Qiao wrote:
> 
> 
> 2011/1/20 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     Qin Qiao wrote:
> 
> 
> 
>         2011/1/20 Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>>>
> 
> 
> 
> 
>            Qin Qiao wrote:
> 
>                Dear all,
> 
>                I would like to try a new forcefield in Gromacs 4.5.3. What
>                should I do after I copied the ff to /share/gromacs/top
>                directory? It seems the original FF.dat doesn't exist in
>         4.5.3..
>                Could you give me some help?
> 
> 
>            pdb2gmx detects forcefield directories by searching for names
>         that
>            end in .ff, then looking in that directory for a "forcefield.doc"
>            file that contains a brief description of the force field.
> 
>            -Justin
> 
> 
>         Thanks. But I cannot find the new forcefield when I used
>         pdb2gmx.. the folder of ff is named 'PACE.ff'
> 
> 
>     It must also contain a forcefield.itp file to be recognized, and
>     ultimately, to work at all.  I did a test of minimum requirements,
>     and only after I added a dummy forcefield.itp file to the test.ff
>     subdirectory did pdb2gmx recognize the new force field.
> 
>     -Justin
> 
> 
> There is an .itp file in the ff.. but it doesn't work.. strange.. is 
> there any other possibility?
> 

It works just fine for me.  To be sure, I used the name "PACE.ff" instead of my 
generic "test.ff" to make sure capitalization or something foolish wasn't a 
problem.  It worked fine, adding "PACE" as entry 16 in the pdb2gmx menu (I also 
have another custom force field, so the order of your pdb2gmx output may be 
different).

The other thing to try is to build the force field in your working directory and 
see if pdb2gmx finds it there.  This is, of course, not strictly required (and 
would be very inconvenient), but it could be a useful diagnostic.

-Justin

> 
>                Best,
> 
>                Qin
> 
> 
>            --     ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://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 <http://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

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



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