From owner-chemistry@ccl.net Fri Feb 18 10:27:00 2011
From: "Heribert Reis hreis-,-eie.gr" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: Problems with adding hydrogens
Message-Id: <-43980-110218102319-12725-6l8OPyqulokhrBtE7fwGfg:_:server.ccl.net>
X-Original-From: Heribert Reis <hreis||eie.gr>
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Date: Fri, 18 Feb 2011 17:12:33 +0200
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Sent to CCL by: Heribert Reis [hreis.:.eie.gr]
Hi 

I need to add Hydrogens to a large number of pdb-files, which all
contain the same molecules in different configurations (the results of
molecular simulation run with implicit hydrogens). I use babel with the 
'add hydrogen' option, which usually works fine, but sometimes 
interprets a -C-C- group as -CH=CH-, instead of -CH2-CH2- group, and
adds only 2H instead of 4. Is there a way to correct this? For example,
can I tell babel explicitly to treat a C-atom as sp3, and not as sp2?

Thanks for any suggestions,
Heribert