AMBER: DNA RNA recognition problem

From: Steve Seibold <>
Date: Thu, 19 Jul 2007 09:51:43 -0400


I am trying to load in a DNA/RNA hybrid + one stand-alone ATP molecule.
The stand-alone ATP molecule I am having no problems with since I have
the parameters that I got online from AMBER. However, for some reason
xleap is not being able to resolve the differences between the DNA and
RNA molecules. Residue 1 through 10 are RNA bases and yet xleap detects
it as a DNA strand and thus, complains. I also added HO'2 thinking this
was the problem, but leap complains that it does not know this type.


Can someone please assist me?


Thanks, Steve

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Received on Sun Jul 22 2007 - 06:07:32 PDT
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