AMBER Archive (2004)

Subject: Re: AMBER: antechamber

From: Xin Hu (
Date: Thu Jul 15 2004 - 21:51:26 CDT

> > I have another question, for a protein comlexed with ATP, the xleap
> > recognize the ATP, do I need to process the ATP as an usual molecule
> > antechamber?
> You could do that, but check the "contributed parameters" page (link from
> the Amber web page.) That has parameters from Heather Carlson's group and
> references to the paper they published on this. Such parameters should be
> better than what you will get from antechamber.

Hi David,
Thank you for the note. There is a problem when I use Carlson's ATP
parameters. Since the added hydrogen atom names are different from these in
my ATP.pdb file, when I try to load my ATP, the xleap still complain there
are a number of hydrogen atom names not found in ATP.prep template. Is there
an easy way to fix the problem?

Thank you for your help!


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