Hi Mikyung Seo,
> 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.
So it works, good for us ;-)
> 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?
We got the charges for each orientation. As they were different we decided to apply
4-orientation RESP fit. That's it...
> What is criteria to choose these 3 'well-defined' atoms?
- Scientifically ? No-one !
- Convenient way: use only heavy atoms selected more or less randomly...
=> Shocking ? well yes and no ;-)
because with Gaussian/GAMESS everybody believes the minimum orientation is unique and it
is wrong !!! Do not forget that RED has been written to allow the derivation of "reproducible"
charges.
> I think that choosing orientations is really important to reproduce
> charges.
Well it is why we wrote RED to control the minimm molecular orientation...
> 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?
Well your charges will be different from the ones available in the Cornell et al. paper, but they
will be reproducible (if you provide the orientation(s) you used) and the Cornell et al ones are
not ....
> 3. Based on your last reply, multi-orientational RESP fit would give
> more general RESP values....
Yes, at least it make sens. However, it has not been tested.
> That means that it is better to use as many orientations as possible?
> How many orientations?
Now with 2 last questions you mixed up two thinks: "reproducibility" and "effectiveness". It
simply makes sens to use multi-orientation RESP fit if charge differences are observed for
different orientations. In our paper, we have examples using up to 12 orientations. It is up to
the user... Do not mix up "reproducibility" and "effectiveness". "Effectiveness" is obained with
multi-conformational RESP fit... In the new RED version we mix multi-orientational and
multiconformation RESP fit to associate charge "reproducibility" and charge "effectiveness".
We have a beta version. If you want to test it let me know....
Kind regards, Francois
F.-Y. Dupradeau
--
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
--
http://www.u-picardie.fr/labo/lbpd/fyd.htm
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu May 06 2004 - 23:53:00 PDT
