Qin Qiao wrote:
2011/1/21 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Qin Qiao wrote:
2011/1/21 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto: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>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto: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
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.
Your first post said that you were using 4.5.3 - does this mean you have
multiple installations after all? If nothing else, you should just upgrade to
4.5.3 and try again. There have been various bug fixes and such that you should
take advantage of.
Beyond that, I have no idea what's wrong. If creating a .ff directory in your
working directory didn't do it, then I'm out of ideas. I've been using that
mechanism for quite a while with no problems.
-Justin
--
========================================
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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