[gmx-users] Porting CHARMM topologies and parameters
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 17 13:15:41 CEST 2006
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.
>>> For residue topology (.rtf) files, you need to consult those of
>>> Yuguang Mu, available here
>>>> 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.
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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