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

[Qin Qiao]

2011/1/20 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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
>
>
>> 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..



>               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
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
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>>    Please search the archive at
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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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