AMBER Archive (2004)

Subject: Re: AMBER: contributed parameters

From: Shau Grossman (
Date: Thu Feb 19 2004 - 20:55:46 CST

Dear Francois,

I have tried both approaches that you have suggested below. I have more
questions in the following:

1) My concern for using the first approach is that C1' atom bears a fairly
large negative charge, and the nearby atoms of the modified base (close to
C1') are also affected to some noticeable degree. Secondly, if I were to
use the
RESP charges generated using the first approach, do I define a new residue
in xleap for the modified nucleotide?

2) If I were to use the second approach as you mentioned with the
restraint of .126 (during the second stage, I assume), I
would then assign these RESP charges to the base atoms in the PREP module
as suggested in JACS, 119, 7095-7104). My question is that what charges I
would use for C1' and H1' atoms in this case.

Appreciate your help very much,

On Wed, 18 Feb 2004, FyD wrote:

> Dear Shau,
> > If one would like to generate his or her own RESP charges for
> > pseudouridine or any modified nucleotide using Amber 7. How would one
> > go about it?
> -1-
> You could apply the strategy detailed in Cieplak et al. J Comput Chem 1995 16
> 1357-1377. In particular see the 'Summary page' 1367. In such startegy, you need
> to use 2 different Electrostatic Potential (from dimethyphophate and your
> modified nucleoSIDE) and you use inter-molecule restraints (see Figure 2).
> -2-
> A different approche would be to use your modified base with a methyl group
> (instead of the sugar) and use a restraint of .1268 (representing the backbone)
> for it as it is demonstrated in Spector et al. JACS 1997 119 7095-7104.
> The second approch might be more simple and will demand really less computer
> time.
> Regards, Francois
> F.-Y. Dupradeau
> --
> The Scripps Research Institute, San Diego, CA
> Faculte de Pharmacie, UPJV, Amiens, France
> --
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