Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

From: case <>
Date: Fri, 8 Jul 2011 23:08:23 -0400

On Sat, Jul 09, 2011, Andre Serobian wrote:
> useboundsfrom(b, m, "1:1,5:??,H?ˆ’T]",getpdb( /usr/local/amber11/dat/dgdb/basepairs + "at.XXIII.pdb" ),"::??,H?[ˆ’T]",0.1);

You have to put quotes around the /usr/local/amber....pairs argument to
getpdb. Also, the first atom expression is garbled, looks like perhaps a
missing "[". The example in the book has a very complex atom expression --
you should either figure out what everything means, and/or start with simpler

Note that simplifying things in other ways can be a good debugging option,

molecule m1;
m1 = getpdb( ....);

Then use m1 as the fourth argument to useboundsfrom();

Tracking down errors like this often takes a lot of divide and conquer work.


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Received on Fri Jul 08 2011 - 20:30:04 PDT
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