AMBER Archive (2006)

Subject: AMBER: minimalization prior to nmode analysis, is it necessary?

From: Magne Olufsen (
Date: Wed Jan 04 2006 - 11:42:21 CST

Hello everyone!

I have calculated the entropy of snapshots with nmode, and I have seen that
I got much lower TS values if I increase minimalization the structures
before I run nmode. I know it says in the manual that one should minimize
the structures prior to the nmode analysis, but why should the snapshots
have to be minimized prior to nmode analysis? The structure is not
minimized when the mm_pbsa energies are calculated. Which convergence
criteria is reasonably to choose? I have a complex of en enzyme which is
223 amino acids and a ligand which consist of several 19 DNA bases.

I hope someone have some suggestions or can tell me which articles to read...

Greetings from Magne Olufsen, Ph.D student, University of Tromsų, Norway

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