[gmx-users] How to install a new Forcefield in Gromacs 4.5.3
Qin Qiao
qiaoqin47 at gmail.com
Fri Jan 21 03:17:07 CET 2011
2011/1/21 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:
>>
>>
>>
>> 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:
>>
>> 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?
-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>
>> <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> <http://vt.edu> | (540)
>> 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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