Re: [AMBER] Modified Nucleic Acid

From: David A. Case <>
Date: Thu, 25 Jul 2013 10:52:28 -0400

On Tue, Jul 23, 2013, Mark Zottola wrote:
> 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
> correct?

Most of the relevant commands have an argument that points to a library, which
should (usually) be 'nab10.lib' nowadays. You might want to consider
installing AmberTools in a disk area you control, since you'll probably be
making modifications.

> 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 you have a modified nucelotide at chain ends, then these would be needed.

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

There is very little discussion in the manual about modified nucleotides; but
nab reads Amber's .lib format, so it should be possible to get it to do what
you want. Simplest route is to edit $AMBERHOME/dat/leap/lib/nab10.cmd to
add new residues, then type "tleap -f nab10.cmd" to re-make the nab.lib

...good luck....dac

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Received on Thu Jul 25 2013 - 08:00:03 PDT
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