[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 
> 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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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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