VMD-L Mailing List

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Jul 09 2009 - 19:17:09 CDT

Thanks, Peter.
Yes, I understand the force field part. I was wondering about the charmm
side of things (should have been more clear on that). In any event, you
did answer my question.
For now, I guess I'll just use amber prmtop/inpcrd files produced with
antechamber.
Thanks

Sasha

Peter Freddolino wrote:
> Hi Sasha,
> you need to distinguish between the force field and MD program that
> you're using. NAMD can be used with the charmm, OPLS, or amber force
> fields (among others). Antechamber lets you get parameters easily for
> use with the amber force field, so if you want to use the amber force
> field, you can just use antechamber (there's an interface for it in the
> molefacture plugin). If you want to use the charmm force field, you'll
> need to use paratool to get your parameters, which does require Gaussian
> or GAMESS. Please note that the latter is freely available (although I
> forget whether the gamess interface in paratool is finished -- perhaps
> Jan can comment).
> Best,
> Peter
>
> Sasha Buzko wrote:
>
>> Hi all,
>> I need to run MD of several protein-ligand complexes, and I wonder if
>> there is a general purpose compound parameter preparation tool. I did
>> see a parameterization interface included with VMD, but it requires
>> Gaussian/GAMESS (which we don't have).
>> For use with Amber, I could do it with antechamber. Is there anything
>> similar that could be used to get compound parameters for NAMD?
>>
>> Thanks for your help
>>
>> Sasha
>>
>>
>>
>
>
>