[gmx-users] Porting CHARMM topologies and parameters
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 17 07:28:09 CEST 2006
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
> 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users