From owner-chemistry@ccl.net Thu Aug  2 15:19:00 2007
From: "lrf2103- -columbia.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
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Date: Thu, 02 Aug 2007 11:02:33 -0400
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Sent to CCL by: lrf2103{=}columbia.edu
Hi Max,

There are lots of programs out there to do this, but your choice
will depend on how accurate you want the positions to be, and how
user friendly it should be. "Reduce" is a very easy-to-use program,
available from the Richardson lab at
http://kinemage.biochem.duke.edu/software/README.reduce.html.

If you want to get very accurate positions for the rotable
hydrogens, I did a survey of several of the methods that might help
you choose (Proteins. 2005 Nov 1;61:296-309). The most accurate
methods I tested were MCCE and Charmm.

Best wishes,
Lucy Forrest

> Hi all
> Does anybody know how I can add hydrogens to a system?
> I've downloaded the pdb file of a enzyme and there aren't
> hydrogen atoms
> (for instance the water molecule is formed only by the oxygen).
> I'd like to saturate my system with the missing hydrogens.
> Any tips will be very appreciated.
> thanks a lot
> MP
>