AMBER Archive (2004)

Subject: Re: AMBER: R.E.D. II to Vlad

From: FyD (
Date: Wed Sep 15 2004 - 11:25:44 CDT

> Thanks a lot for all the answers. This discussion is very helpful.
> Indeed, the most worrying is the charge on the N1 and C6 atoms of RG.
> This charges are -0.4787 and 0.4770 in the amber RG residue. When I
> calculated these charges using a C3'endo G nucleotide without any
> orientation I got -0.5754 and 0.5691.

The optimized structure is _always_ reoriented. If the rigid body reorientation
algo. is not selected the internal algo. implemented in GAMESS or in Gaussian
is selected... This was the former way to derive RESP and ESP charges before
R.E.D. As an example in Gaussian, the molecular orientation of the optimized
structure is the 'Standard orientation'... Francois
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