On Wed, Sep 25, 2002, Masaki Tomimoto wrote:
>
> When I try to go to MM/PBSA calculation with a small molecule, As far as I
> understand, in order to get an appropriate energy parameter for the small
> molecule, I need to use antechamber. Right? In this case, Tripos-Mol2 file
> is an appropriate input format to antechamber, isn't it? If so, does
> antechamber use atom definitions in Tripos-Mol2 file? In other words,
> energy parameters generated by antechamber depend on atom definitions in
> Tripos-Mol2 file?
>
No: generally you want antechamber to re-determine the atom types (using the
gaff force field), since we don't support the sybyl force field. Hence,
the only real information antehcamber will use from the mol2 file will be
atom names, bond connectivities, residue name, and coordinates.
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Thu Sep 26 2002 - 08:28:51 PDT
