AMBER Archive (2007)

Subject: AMBER: DNA RNA recognition problem

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Jul 19 2007 - 08:51:43 CDT

Hi AMBER

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




  • application/octet-stream attachment: leap.log
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu