AMBER Archive (2003)

Subject: Dummy atoms in free energy calculation

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Sat Jan 11 2003 - 12:18:44 CST

Dear AMBER community,
I'd like to ask about what rules there are for choosing the parameters for
dummy atoms. Specifically, I have an H1 atom and a dummy "attached" to it.
This will be "mutated" into OH - HO. For the dummy, should I use both the
bond parameters as in OH-HO or just the equilibrium value or totally
different? What then? What about other parameters?

Or could yopu point me to some literature where this problem is dealt with?

Thank you in advance,

   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