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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Received on Thu Feb 20 2003 - 00:53:01 PST
