[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:
> 
> 
> 
>         2011/1/21 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:
> 
> 
> 
>                              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>>>>
>                       <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 <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
> 
> 
> Thanks. The version is 4.5.1, but it just doesn't work.

Your first post said that you were using 4.5.3 - does this mean you have 
multiple installations after all?  If nothing else, you should just upgrade to 
4.5.3 and try again.  There have been various bug fixes and such that you should 
take advantage of.

Beyond that, I have no idea what's wrong.  If creating a .ff directory in your 
working directory didn't do it, then I'm out of ideas.  I've been using that 
mechanism for quite a while with no problems.

-Justin

> 
>     -- 
>     ========================================
> 
>     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

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