AMBER Archive (2003)

Subject: Minimization after dynamic?

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Wed Feb 19 2003 - 18:13:31 CST

 Dear AMBER Users,

 I made a question some days ago asking if it is really
necessary to do a final minimization step after a dynamic
procedure.
 Dr. Case answered me that it depends on the research
focus, whether I was interested to study the final
coordinates minimized or the conformers' properties of the
dynamic procedure.
 Well, after performing my molecular dynamic protocol I
will try to describe some DNA properties from 3D QSAR
models. I will define some 'chemical probes' to interact
with it and the final goal is try to understand the
mechanism of molecular recognition between DNA-drugs and
DNA-macromolecules.
 So I would like to know if the conformes got from dynamic
is a good starting point to me or I have to minimize them.
 Thank you very much,

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

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