AMBER Archive (2004)

Subject: Re: AMBER: contributed parameters

From: Shau Grossman (
Date: Fri Feb 20 2004 - 15:46:04 CST

Dear Francois,
> Yes it seems strange. When I applied this 1st startegy on my unusual nucleotide
> I got similar charge values that those reported in table VI page 1368.

If I were to reproduce the results in table VI page 1368 applying the
summary page 1367,

1) Do I apply the intermolecular restraint for phosphate-joints to
each nucleoside (G,C,A,T) and at the same time (in the first stage) the
intermolecular sugar equivalencing restrain (except C1' and H1') is
applied to the four nucleosides?

2) If the approach in 1) is correct, would adding modified nucleotides on
top of four regular nucleosides (G,C,A,T) and using the similar strategy
- I mean if I should still expect similar charges for the four bases and
their C1' and H1' atoms as generated in 1)? Is that how you applied your
unusual nucleotide?


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