[gmx-users] How to install a new Forcefield in Gromacs 4.5.3
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 21 03:10:10 CET 2011
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?
-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
>
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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
>
> ========================================
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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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