Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

From: case <>
Date: Fri, 8 Jul 2011 08:41:39 -0400

On Fri, Jul 08, 2011, Andre Serobian wrote:

> molecule m;
> bounds b;
> m = fd_helix( "abdna", "atgcat", "dna" );
> b = newbounds ( m, "at.XXIII.pdb");
> useboundsfrom(b, m, "1:1,5:??,H?ˆ’T]", get-pdb( PATH + "at.XXIII.pdb" ), "::??,H?[ˆ’T]", 0.05 );

You want "getpdb", not "get-pdb". Be sure that PATH is somehow expanded
to a valid string: easiest is just to spell out the entire path, or copy
the at.XXIII.pdb file to the local directory. [I see that the example on
p. 313 has a hypenation error caused by the formatting program.]

It is also true that NAB is not all that helpful when there are syntax errors
in the code. A common strategy is to look at the end of .c file, in order to
get some more clue about what is going on.

...hope this helps...dac

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Received on Fri Jul 08 2011 - 06:00:05 PDT
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