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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