AMBER Archive (2004)

Subject: Re: AMBER: nucgen generated RNA duplex: leap problems

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 20 2004 - 13:26:17 CDT

On Tue, Apr 20, 2004, Arvind wrote:
> i generated an Arnott A-RNA duplex with the sequence (CGCAAAUUUGCG) using
> the following nuc.in file:
>
>
> NUC 1
> R
> C5 G C A A A U U U G G G3
                                                   ^^^
>
> NUC 2
> R
> C5 G C A A A U U U G G G3
                                                   ^^^

You have a typo in your input, and are trying to generate G-G pairs. Nucgen
assumes Watson-Crick pairing. One way to catch this would be to look visually
at the output pdb file to see what is going on.

Another way would be to look carefully at the error messages:

> Warning: Close contact of 1.998597 angstroms between .R<RG 2>.A<H22 25>
> and .R<RG 23>.A<H22 25>

This tells you of a bad contact between Guanine 2 and Guanine 23. But you
don't want residue 23 to be a guanine.

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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