AMBER Archive (2009)

Subject: Re: [AMBER] loading PDB of a RNA sequence

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 08 2009 - 06:38:34 CDT

On Tue, Sep 08, 2009, gunajyoti das wrote:

> Â I have tried to load a RNA sequence obtained from the PDB file 1DRZ,
> but xleap colud not generate the prmtop and inpcrd files. When i tried a
> DNA sequence i could generate the prmtop and inpcrd files.

I am guessing(?) that you used a standard leaprc command. In the old days,
you had to use an "rna" version (since the old PDB nomenclature didn't
distinguish between DNA and RNA). If you apply bugfix.12 in AmberTools,
then the leaprc.ff99SB and leaprc.ff99bsc0 files should be able to read either
DNA or RNA.

As Carlos pointed out, though, it is difficult to trouble-shoot, since you
provided so little information on what you actually did.

...dac

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