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

[Justin A. Lemkul]

Qin Qiao wrote:
> 
> 
> 2011/1/21 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:
> 
> 
> 
>                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>>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>                <mailto: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>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
>                       <mailto: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
> 
> 
>         Thanks. But it doesn't work.. and I tried to copy the exact
>         files in the charmm.ff to a new test.ff, and pdb2gmx doesn't
>         find test.ff..
> 
> 
>     Do you have multiple versions of Gromacs on the same machine?  If
>     so, are you calling the right pdb2gmx?
> 
> Could you tell me how can I tell which version of pdb2gmx I call?
> 

pdb2gmx -h

-Justin

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

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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