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

[Qin Qiao]

2011/1/21 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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
>
>
> Thanks. The version is 4.5.1, but it just doesn't work.

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