Qin Qiao wrote:
2011/1/20 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Qin Qiao wrote:
2011/1/20 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@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
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
========================================
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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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