[gmx-users] Porting CHARMM topologies and parameters
jhenin at vitae.cmm.upenn.edu
Thu Aug 17 16:57:07 CEST 2006
On Wednesday 16 August 2006 23:43, 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.
> For residue topology (.rtf) files, you need to consult those of Yuguang
> Mu, available here
Thanks a lot for the info! I will try that. From what I see, there might be
some work left on the residue topology conversion.
> > 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.
I have a problem with that, though. I did look in the manual, and Urey-Bradley
potentials are mentioned in chapter 4, but I cannot see any reference to them
in chapter 5. For instance, table 5.4 lists all bonded interactions, and none
of the 3 angle potentials there is Urey-Bradley. But it seems that combining
a harmonic angle with a harmonic potential (bonds, type 6) is a clean way of
obtaining that result.
Have I missed something?
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