Jerome Henin wrote:
On Wednesday 16 August 2006 23:43, Mark Abraham wrote:
Jerome Henin wrote:
Hi all,
As quite a few people have done before, I am about to try and convert a
CHARMM topology into a GROMACS one. To that effect, I will probably need
one or several programs that will do part of the job. When these are
done, I suppose they might be of interest to others on this list.
Since I am not keen on the idea of reinventing the wheel, I would like to
know if there is an existing base I can build on. Have you guys been
doing something of the sort? Using what tools?
I have previously made available under GPL two perl scripts; one that
convert CHARMM parameter files into GROMACS parameter files (.itp), and
another that corrects the output of grompp to achieve correct treatment
of U-B terms, 1,4 LJ terms and multiple periodic dihedrals. The former
now works on a range of CHARMM parameter files. I attempted to update
the link on the GROMACS web page today, and it has disappeared,
presumably awaiting moderation. Please mail me off-list for a updated
copy if they don't appear in the next few days. There's no change to
their function, but the former script now accept a wider range of inputs.
For residue topology (.rtf) files, you need to consult those of Yuguang
Mu, available here
http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.
tar.gz
Thanks a lot for the info! I will try that. From what I see, there might be
some work left on the residue topology conversion.
A side question: does is sound reasonable to emulate Urey-Bradley angle
potentials by adding an extra "bond" term?
U-B angle potentials are implemented natively in GROMACS - see chapters
four and five in the manual. There are of course a few ways you could
hack an emulation of them.
I have a problem with that, though. I did look in the manual, and Urey-Bradley
potentials are mentioned in chapter 4, but I cannot see any reference to them
in chapter 5. For instance, table 5.4 lists all bonded interactions, and none
of the 3 angle potentials there is Urey-Bradley. But it seems that combining
a harmonic angle with a harmonic potential (bonds, type 6) is a clean way of
obtaining that result.
Have I missed something?
Thanks,
Jerome
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it's there. angle type 4 or 5, try it and check your tpr file. sorry
that the documentation is a bit outdated.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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