AMBER Archive (2007)

Subject: AMBER: Polarizable potential

From: Denis Courtier (amber982_at_gmail.com)
Date: Wed Nov 28 2007 - 08:32:49 CST

Hello,

I have make some questions about polarizable potentials, but i have not
still clear some basic ideas

I am trying to mimic a N-Ac proline molecule into a polarizable potential.
As I have understood, first i have to optimize my molecule at HF/6-31G*,
compute ESP by B3LYP/cc-pVTZ and finally, fit the charges by RESP. Then, use
SANDER.

When i run leaprc.ff02polEP.r1into xleap, Am I charging polarizable
parameters for any molecule? In this case, which are these molecules?

or

Am I only charging the method to compute them? And, Do I still need to
paramatize my system?

If I have to parametizer my system before, can anybody tell me where can i
find a guide for all the steps.

Thank you.

Denis.

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