[gmx-users] Porting CHARMM topologies and parameters
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 17 17:08:47 CEST 2006
Jerome Henin wrote:
> 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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it's there. angle type 4 or 5, try it and check your tpr file. sorry
that the documentation is a bit outdated.
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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