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
--
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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Received on Wed Feb 18 2004 - 17:53:00 PST
