[gmx-users] Porting CHARMM topologies and parameters

Yang Ye leafyoung81-group at yahoo.com
Thu Aug 17 10:24:05 CEST 2006

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.
>> 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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