[gmx-users] Porting CHARMM topologies and parameters

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 17 05:43:47 CEST 2006

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.

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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