AMBER Archive (2005)

Subject: Re: AMBER: amber question about leap

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 02 2005 - 10:05:12 CDT

On Thu, Jun 02, 2005, du yongchun wrote:

> I use leap in AMBER 7 to read the following PDB file:tyr.pdb
> xleap
> >source leaprc.ff02
> >x=loadpdb tyr.pdb
> the output is as the follewing:
> Loading PDB file : ./tye.pdb
> Added missing hervy atom : .R<CTYR 232>.A<OXT 22>
> total atoms in file:12
> ..............
> the residue name in the pdf file is TYR ,but in xleap ,it changes to CTYR
> and add an atom OXT.I don't know why it is.Can you tell me why and how can
> I modify it.Thanks!

Look at the leaprc.ff02 file: is has commands that make the final amino acid
CTYR if it is entered as TYR. You need to remove the "addPdbResMap" lines
from your leaprc file if you do not wish to have such a translation made.

...good luck....dac

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