Re: [AMBER] DNA with NAB

From: Jio M <>
Date: Fri, 25 Oct 2013 07:14:34 -0700 (PDT)

Dear David

Thanks for reply. I tried my file having xyz points like this:
./a.out < my.dat  > temp.txt

In tmp.txt I get some points which should be the points for placing the base pairs (please correct me if wrong). Further:

1) There are other two related programs (12 and 13). How do I input temp.txt points to program_12? and further to use program13 .

2) Where I can provide the desired sequence of DNA? seems to give random sequence if used with program_13 (nab

3) Also I am curious: 
>> That said, I'm trying to get them updated to a more useable form
is it expected soon? approx. time. For me I think nab is somewhat difficult to start with.

Thanks and regards,

On Friday, October 25, 2013 12:50 AM, case <> wrote:
On Tue, Oct 22, 2013, Jio M wrote:

The program_11 requires an input file; if you just do the above, it will just
hang waiting for it.

> 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?

You can use this file, e.g. a.out < toto.dat, but I think that tot.dat is
actually the output from some earlier run.  You can try to define various
paths (x,y,z on each line of an input file), and see what you get.

Unfortunately, time has degraded some of the NAB examples--now they are
templates for ideas about how to write NAB programs than they are useful
scripts per se.  That said, I'm trying to get them updated to a more useable

...regards...dave case
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Received on Fri Oct 25 2013 - 07:30:03 PDT
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