AMBER Archive (2003)

Subject: Polarization charges -geometry

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Fri Jan 17 2003 - 02:21:30 CST

Hello there,
I have a question on the best practices to derive charges for use with
polarization FF (ff02). I know
that I should use B3LYP/cc-pVTZ//HF/6-31G* BUT I have a neutral inhibitor of
100 atoms.

For it might take a month to optimize it on HF level, I'd like to ask what
of the following possibilities (or even
different one) are best to use. Either I can optimize it on RI-DFT level
(what basis set?) and then apply HF (is
it necessary?). Or I migh optimize only added hydrogens (the rest is from
crystal structure of the complex).
Or I may leave it as it is and just calculate charges. Alternatively, I
could "decompose" the inhibitor into parts,
cap them to be neutral, optimize (or not?) them and calculate charges for
the parts.

Or should I use multi-conformation fitting? How should I choose the
conformations in that case?

Just a short question on non-polarizable charges: should the structure (or
hydrogens) be minimized first?
On what level/basis set?

Could you please advice me? Do you have a guess what might be the
differences among the above approaches
for use in MD runs and MM-PBSA analysis?

Thanks.

All the best,

   Martin

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Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem