David van der Spoel wrote:
Yang Ye wrote:
David van der Spoel wrote:
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.
the files can be downloaded now from Download/Contributions/Software
The link doesn't lead to downloading of file.
just click something like that.
It works now!
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
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.
Mark
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