[gmx-users] Porting CHARMM topologies and parameters

[Yang Ye]

David van der Spoel wrote:
> 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.
It works now!
>
>
>>>
>>>>
>>>> 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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