[AMBER] Modified Nucleic Acid

From: Mark Zottola <mzottola.gmail.com>
Date: Tue, 23 Jul 2013 11:18:01 -0400

I have read through, perhaps unsuccessfully, the NAB documentation to
understand how to build a DNA sequence with a modified nucleic acid (or

It seems the program reads a library file to get coordinates to build the
structure desired. As I am on a shared system where one cannot just modify
libraries at will, it seems there must be a variable on can set to point to
a local copy of a library in order to generate a structure. Is this

Assuming this is correct, which library should I copy?
In contrast to antediluvian incarnations of AMBER (where the phosphate
linkage was considered separate from the nucleoside), it seems I need to
build the entire phosphorylated structure. Is this correct? Should I
develop residues for 3' and 5' ?

If this is covered in the NAB part of the tools manual, a pleasant pointer
to that section for re-reading would be welcome.


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Received on Tue Jul 23 2013 - 08:30:03 PDT
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