Re: AMBER: PDB file format for AMBER

From: David A. Case <>
Date: Sat, 7 Apr 2007 08:56:18 -0700

On Fri, Apr 06, 2007, Neelanjana Sengupta wrote:
> Is there a way to directly convert .pdb files with CHARMM-type atom names,
> to a format adopting AMBER-type atom names? (I would think that a lot of
> people face this issue frequently, and am hoping that there is a
> straightforward way to do the conversion). Any help or pointers is
> appreciated.

Try using protonate: that should fix up all of the hydrogen names. I'm not
sure whether CHARMM uses a non-IUPAC name for the CD1 atom of ILE or not, but
that is easy enough to fix by hand.

...good luck...dac
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Received on Sun Apr 08 2007 - 06:07:50 PDT
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