AMBER Archive (2006)

Subject: AMBER: change atom in a DNA double strand

From: Carra, Claudio \(JSC-SK\)[USRA] (claudio.carra-1_at_nasa.gov)
Date: Wed Jul 05 2006 - 16:09:23 CDT

Dear All,
I'd would like to modify an atom of residue in a DNA double strand.
The initial geometry from the canonical structure generated by
nucgen is absolutely fine, but than, I'd like to have a guanine in
the middle of the double strand replaced the corresponding oxidized one.

it is easy to generate a new library with antechamber for a small
molecule, but
I didn't find any example where a new molecule (not atom) is inserted
into a
macro system.

The error I get and I can't fix is relative to missing parameters
for the force field, which in general can be fixed by loading frcmod
file, but not in this case.

I've followed the very nice tutorial
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/
but unfortunately it seems useful to my case.

I believe that to have the chance to modify even an atom
to a given structure can be very interesting to study bio systems
chemically altered, by oxidation for instance.

thanks a lot in advance
sincerely
Claudio

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