Re: AMBER: Modified nucleotides

From: FyD <>
Date: Wed, 14 Feb 2007 13:30:50 +0100

Quoting mathew k varghese <>:

> I am trying to do the simulation of a DNA molecule (NMR structure).
> Some of the bases contains an extra ring. We have tried to do a
> Gaussian calculation but I could not get the ESP charges from the
> output. That is why I am asking the question.
> The pdb files of the molecules are attached.
> Would you please direct me how to do the charge calculation?

You can use R.E.D. and look in
R.E.DD.B. for examples of
RESP or ESP charge derivation. See for instance the following
R.E.DD.B. projects:
from Jingyang Chen: F61 up to F-64
or F-57 up to F-60
See F-60 for more complex examples

You have many different examples of RESP (different values of qwt
values with one or two RESP stages) and ESP charge derivation.
Use the "List projects" tools and theb select "Molecule fragment" and
then "Display".

regards, Francois

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Received on Sun Feb 18 2007 - 06:07:05 PST
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