AMBER Archive (2003)

Subject: Side-chain/main-chain decomposition in MM-GBSA

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Thu Apr 03 2003 - 02:24:35 CST

Dear AMBER commmunity,
I'd like to ask about the way the decomposition to side-chain and main-chain
contributions is done in MM-GBSA calculations.

I assume for protein (let's say in parm99) it's straightforward; N,H,C,O
atom types are considered main chain, the rest is side chain.
But how is it for ligands and gaff? Is it n,hn,c,o? Can it tailored (so as
to add some atom types)?

Or is prepin Main chain information taken into account?

Thank you in advance for your responses.

All the best,

Martin
------------------------
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