AMBER Archive (2004)

Subject: AMBER: choosing 3 atoms for reorientaion in R.E.D

From: Mikyung Seo (seo_at_ualberta.ca)
Date: Thu May 06 2004 - 16:38:19 CDT

Hello Francois,

Thanks a lot for your explanation and example provided.

I tested charge reproducibility using different sets of Cartesian coordinates
with your EtOH example (with 4 reorientations for EtOH).
The charges were reproducible with 4 reorientations for EtOH.
When I tested without 4 reorientations I got different charges set for
different sets of Cart. coord. as I expected.

I have questions as following:

1. How did you select 3 atoms and 4 reorientations (ex.EtOH) for the
rigid-body re-orientation algo. in R.E.D?
What is criteria to choose these 3 'well-defined' atoms?
I think that choosing orientations is really important to reproduce charges.

2. If I chose 3 well-defined atoms and reorientations for already published
molecules (ex. Cornell et al, 1995) and run using the rigid-body reorientation
algo. in R.E.D, would I have reproducible charges for published molecules?

3. Based on your last reply, multi-orientational RESP fit would give more
general RESP values....
That means that it is better to use as many orientations as possible?
How many orientations?

Thanks again.
Mikyung

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