Re: AMBER: reorientation in R.E.D

From: FyD <>
Date: Wed, 05 May 2004 19:55:51 +0200 (CEST)

Dear Mikyung Seo,

> There are 6 different orientations for N-Methyl-Acetamide example in
> R.E.D(1.0) tutorial.
> How can I get this reorientation information (6 different number
> sets)?

You are right that is a first key point.

If you decide to choose the ab-initio re-orientation algo. [i.e. by placing the
center of nuclear charge at the origin (available in Gaussian) or using the
molecular principal axes (available in GAMESS)] you have at least two problems:

- You can get different minimum molecular orientations generated by the 2
ab-initio software => the charges derived using GAMESS and Gaussian (geometry
optimization & MEP computation) will be different (moreover, the values of such
differences are un-predictable). That is the first problem.

- Even using one particular software (i.e. GAMESS 'OR' Gaussian, this time), a
constant molecular orientation for the same minimum cannot be generated whatever
the model studied is. If we take the example of Gaussian (because it is mainly
used by the AMBER community), different "Standard orientations" can be generated
by Gaussian for the same minimum: Thus, different set of charges will be
generated for the same minimum. Once again, the charge diff. are not
predictable. That is the second problem.

- Thus, we implemented in prog. R.E.D. a rigid body re-orientation algo. based
on three atoms that is applied after geometry optimization. If this
re-orientation algo. scheme is selected (by providing 3 'well defined' atoms in
the starting PDB file), the charges will be reproducible because the minimum
molecular orientation is known whatever the ab-initio software is (accuracy
reached = 0.0001 e; i.e. the format of the charge values reported in a ".prep"
or "OFF" files for the Cornell et al. FF). That is the main idea.

> How can I know which molecule needs reorientation or not?

Once again, that is an important point, you are right.

- The first idea is that charges which are published must be reproducible
whatever the ab-initio prog. is. This is achieved when the rigid-body
re-orientation algo. is applied. Thus, people have to publish the molecular
orientation used in the RESP or ESP fit WITH the set of RESP charges.

- The second idea is the multi-orientational RESP fit. The question you asked is
 more or less why selecting one orientation and not another one ? If quite
different atomic charges are observed for two different minimum molecular
orientation, we decided to incorporate a multi-orientational RESP (by analogy to
the multi-conformational RESP fit) fit allowing to average the charge diff.
observed for one orientation over several orientations.

Thus, in the R.E.D. tutorial, you mentionned that a 6 re-orientation RESP fit is
performed on NMA. It was just an example of multi-orientational RESP fit. Once
again, the charges are reproducible because the 6 orientations used in the RESP
fit have to be provided.

Thus, concerning which orientation(s) to select: it is up to the user which has
to report/explain the molecular orientation(s) used in the RESP fit.

I hope it is more clear. Once again, I understand that it is difficult to figure
out the orientational problem without a publication... The corresponding paper
is going to be sent very soon.

Best regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed May 05 2004 - 19:53:00 PDT
Custom Search