AMBER Archive (2003)

Subject: charges, opt and iops

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Sat Feb 15 2003 - 09:59:44 CST

Dear AMBER community,
I would like to ask for details about charge derivation for a ligand.
Ideally, the structures should be optimized
by HF/6-31G*. But what if I have a crystal structure and optimize hydrogens
only or nothing at all?
(adding them reasonably, e.g. in INSIGHT). What would you think about such
charges? (I must say, trajectoruies are stable
but how much could it affect interaction energies?)

My second question is; what is the status with iop(6/42=6) in ESP
calculation? (calculate 6 points per unit area for the ESP, default is 1,
James Caldwell wrote this in the reflector). Should it be used? With both,
ff99 and ff02?

Looking forward to your answers.

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
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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