CCL: Tools to add hydrogens to ligands



Hi,

You can try the 'reduce' program from AmberTools. 
http://ambermd.org

-Dan

On Saturday, December 21, 2013, Bin Sun sunbinxod{:}gmail.com wrote:

Sent to CCL by: Bin Sun [sunbinxod[*]gmail.com]
Hello everyone,
In my experiment ,there are about 200 ligands from PDB without
hydrogens. I need to add hydrogens to them, but the number is too large
so that I cannot add hydrogens manually. I have tried openbabel to add
hydrogens to ligands.When I checked I found that nearly 30% results were
worry. For example, some atom ought to contain three hydrogens but in
fact contained four hydrogens. Are there any free tools in the form of
"command lines" to add hydrogens to ligands more exactly?




Thanks!

Sun



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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)