[gmx-users] Porting CHARMM topologies and parameters

[David van der Spoel]

Yang Ye wrote:
> 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.

just click something like that.


>>
>>>
>>> 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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>>
>>
> 
> 
> 
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-- 
David.
________________________________________________________________________
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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