Re: [AMBER] DNA with NAB

From: Jio M <>
Date: Thu, 24 Oct 2013 12:23:39 -0700 (PDT)

Please let me know if someone tried program 11 nab before?

On Tuesday, October 22, 2013 4:42 PM, Jio M <> wrote:
Dear David

I am trying to exlpore options and started NAB language reference and as number of examples found "wrapping DNA along a path". The set of programs (program 11 to 13) under this section seems to solve my problem and skipping number of sections (sorry) I directly jumped to run program 11 which generate points:

does it take long time for a.out to complete as I am not getting any out file. Or something I am missing?

Also where I should define the new path points to wrap my DNA and the sequence for the same. I saw one file toto.dat in nab examples and I tried to visualize it and it looks like a spiral thing. Is this file an example for some program in nab?



On Monday, October 14, 2013 12:47 PM, David A Case <> wrote:

On Sun, Oct 13, 2013, Jio M wrote:

> I never used NAB. I am not sure whether it can help in generating DNA
> folded structures? Please suggest if someone tried NAB for this?

NAB is a small programming language that offers interfaces to a number of ways
to construct DNA molecules, including rigid body rotations and distance
geometry.  Depending on what you mean by "folded structures", it may or may
not be able to help.  You would usually need some addtional data (beyond
the sequence) to construct useful models of nucleic acids.

AMBER mailing list
AMBER mailing list
Received on Thu Oct 24 2013 - 12:30:02 PDT
Custom Search