On Thu, Aug 11, 2011, Charles Johnson wrote:
> I am currently working through the AMBER tutorials for NMR refinement
> of a DNA duplex. However, I am using RNA and came across this
> statement: If you were working with RNA instead of DNA, you would want
> to source $AMBERHOME/dat/leap/cmd/leaprc.rna instead of the default
> $AMBERHOME/dat/leap/cmd/leaprc (which assumes the nucleic acid residues
> are DNA). I am not sure how or where to implement this change. Any
> help would be appreciated.
The tutorial is out of date. Before the introduction of PDB format 3, the PDB
standard for residue names was the same for DNA and RNA(!), and special
features were needed to tell Amber programs which was which.
This is no longer necessary, if you use an up-to-date leaprc like leaprc.ff10.
Thanks for the reminder that we need to update the tutorial. But as always,
treat tutorials as guides, recognizing that sometimes you need to follow the
spirit, not the letter. Also, be sure you can run (short) unconstrained
simulations of whichever nucleic acid you want, before jumping into restrained
problems.
....dac
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Received on Thu Aug 11 2011 - 15:00:02 PDT
