CCL: Tools to add hydrogens to ligands



 Sent to CCL by: Geoffrey Hutchison [geoffh!A!pitt.edu]
 Hi Sun,
 Well, many people do use Open Babel for exactly this. I'm quite surprised that
 you think 30% of the molecules have issues. But there's a separate
 openbabel-discuss mailing list where you can ask questions and we'd certainly
 like to know about potential bugs.
 So please either e-mail the list or e-mail me directly with some of these PDB
 ligands and let's see what the problem is.
 Thanks very much,
 -Geoff
 ---
 Prof. Geoffrey Hutchison
 Department of Chemistry
 University of Pittsburgh
 tel: (412) 648-0492
 email: geoffh()pitt.edu
 web: http://hutchison.chem.pitt.edu/
 On Dec 21, 2013, at 5:01 AM, Bin Sun sunbinxod{:}gmail.com
 <owner-chemistry()ccl.net> 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