Re: Polarization charges -geometry

From: David A. Case <>
Date: Tue 21 Jan 2003 08:56:07 -0800

On Fri, Jan 17, 2003, Lepsa wrote:

> I have a question on the best practices to derive charges for use with
> polarization FF (ff02). I know that I should use B3LYP/cc-pVTZ//HF/6-31G*
> BUT I have a neutral inhibitor of 100 atoms.

You should see if you can break this up into fragments, then combine them
by hand.

A cheaper, and still "pretty good" approach is to get the ordinary RESP
charges, then scale them all by 0.88. A molecular mechanics (or PM3 or
HF 3-21G) geometry optimization might also be sufficient.

There are certainly trade-offs to be considered. With a 100-atom inhibitor,
you are treading new ground. Try some of the above ideas on a smaller system
(comparing to the full solution), and see how big a difference it makes.

I would recommend (if you have not already done this) do carry out
non-polarizable simulations to provide a base-line for the more elaborate
calculations. Remember that ff02 (and ff02EP) is still very new, and hence
somewhat "experimental" parameterizations.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Tue Jan 21 2003 - 08:56:07 PST
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