Re: AMBER: S-nitrocysteine

From: FyD <>
Date: Wed, 13 Jun 2007 23:44:59 +0200

Quoting Anthony Cruz Balberdi <>:

> I am planning to study a protein that have a S-nitrocysteine. I have
> been search for parameters over the internet without success.

You will find SO3-, SSO3- and SSMe cysteine derivatives in R.E.DD.B.
for the Cornel et all & Duan et al FFs. They are not useful for your
problem but they can be used as examples besides the R.E.D. III

> Then I start a RED job to find the charges for the central
> aminoacid unit using the example in the RED-III tutorial. The
> results: ESP relative RMS (SQRT(chipot/ssvpot)) 0.17655
> output2_m1: ESP relative RMS (SQRT(chipot/ssvpot)) 0.17483.

Here you compare the RRMS value of the central fragment
( to that of the whole molecule (output2_m1) in a single
molecule RED-III job:
The RRMS increase because of the two INTRA-MCC added during the fit is
(0.17655 - 0.17483) !

A strong limitation in R.E.D.-III is that if you want to derive the
central, the N-term & the C-term fragments you need to run 3 RED-III
jobs to generate the corresponding Tripos mol2 FF library precursor.
With R.E.D.-IV this is now carried out in a sinle R.E.D.-IV run and
the corresponding Tripos mol2 files are generated. For update about
R.E.D. IV see "R.E.D.-IV news" from the R.E.D. home page.

> I will use many of the parameters for the cysteine
> central residue but there is some bonds, angles, and dihedral that I
> need to add to the residue. How I could find
> those values??? Any one have the parameters form this residue??

I think you have to derive your own FF parameters...

regards, Francois

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Received on Sun Jun 17 2007 - 06:07:13 PDT
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