AMBER Archive (2007)

Subject: Re: AMBER: DNA RNA recognition problem

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 19 2007 - 10:01:17 CDT

On Thu, Jul 19, 2007, Steve Seibold wrote:
>
> 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.

For RNA/DNA hybrids, you have to explicitly edit your pdb files to use
unambiguous residue names. That is, your DNA residues have to be named
DA, DC, DG, DT, and the RNA ones RA, RC, RG and RU. With the standard leaprc
files, I think you also need to add a "5" to the 5' end and a "3" to the 3'
end of each strand.

See section 3.5.3 of the Users' Manual for more information.

....dac

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