AMBER Archive (2008)

Subject: AMBER: flexible molecule parameterization

From: Zhenwei Lu (
Date: Fri Jan 25 2008 - 09:36:46 CST

I have one flexible ligand which contains negative charge and multiple
hydroxyl group and tried to do parameterization following the amber
protocol. First use HF/6-31G* to optimize the structure from PDB and then
derive the charge. One thing bothers me that two intra-hydrogen bonds were
formed after optimization. The distance between donor and acceptor is 3.5
Angstrom and 2.5 in the optimized structure. I think it will always go this
way since there is no protein environment. On the other hand, I think the
parameter should be the similar for the same ligand no matter where it is
(In the water box or buried in the protein). Here is my question: what
should I do to get the “right” parameter and what’s the effects if I
use the one derived from my optimized structure? Is it OK to fix all the
heavy atoms to do optimization? Or is there some protocol for this kind of
situation? Any suggestion will be appreciated.

Zhenwei Lu
Graduate Student
Biochemistry & Molecular Biology
313 Biochemistry building
Tel: 517-353-8786

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