Re: [Apbs-users] Small molecules

[Nathan B. <ba...@cc...>]

Hello --

Please see PDB2PQR (http://pdb2pqr.sf.net/) and the associated manuals
and tutorials for information on how to use PEOE and related
methodology developed by Nielsen, Klebe, and Czodrowski to
parameterize small molecules.

Good luck,

Nathan

On 10/14/07, Amit <am...@ho...> wrote:
>
> Hi,
> I'm currently working on small non-protein molecules, such as the hormone
> epinephrine and the drug acetaminophen. I am trying to use APBS for
> calculating the solvation energy of those molecules, but I have a problem=
 of
> parameterizing them. I am aware VMD has parameterizing tools, but as far =
as
> I know it uses CHARMM or AMBER forcefields. When calculating solvation
> energies, I usually prefer using the PARSE parameters set, since it was
> obtained specifically for solvation calculations. I know the original PAR=
SE
> set ignores small organic molecules, and I was wondering if there is a
> similar set that can be used instead of the forcefields mentioned above.
> Cheers,
> Amit.
>
>
>
>
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--=20
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/