[AMBER] Creating hoogsteen basepaired DNA using NAB

From: Andre Serobian <a.serobian.unsw.edu.au>
Date: Fri, 8 Jul 2011 17:18:37 +1000

Dear All,

I am trying to create hoogsteen AT / TA and GC / CG base pairs in DNA using NAB the following nuc.nab file is an example:

........................................................................................................................................................................
molecule m;
bounds b;

m = fd_helix( "abdna", "atgcat", "dna" );
b = newbounds ( m, "at.XXIII.pdb");

useboundsfrom(b, m, "1:1,5:??,H?T]", get-pdb( PATH + "at.XXIII.pdb" ), "::??,H?[T]", 0.05 );
useboundsfrom(b, m, "1:2,6:??,H?T]", get-pdb( PATH + "ta.XXIII.pdb" ), "::??,H?[T]", 0.05 );

putpdb( "nuc.pdb", m, "-wwpdb");
........................................................................................................................................................................

There is somthing missing as I get the following error:
"9 Symbol get not declared. nab2c failed!"

I realise this is not the right way to use the distance geometry method to create the DNA. If anyone can help or point me in the right direction with how to create hoogsteen base paired DNA with NAB it would be much appreciated.

Another method I have tried is to create the regular watson-crick DNA and then manually orientate the bases in xleap to mimic hoogsteen pairs. However I am not sure whether the program will override this change and revert back to waston-crick orientation in MD runs since the DNA was created with waston-crick templates in the first place.

Thankyou in advance for any assistance.

Kind regards,

Andre


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Received on Fri Jul 08 2011 - 00:30:03 PDT
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