From owner-chemistry@ccl.net Sat Dec 21 16:00:00 2013 From: "Daniel Roe daniel.r.roe-x-gmail.com" To: CCL Subject: CCL: Tools to add hydrogens to ligands Message-Id: <-49474-131221121040-19305-Ii1/JNW9XCKJtAQwiGP20A%a%server.ccl.net> X-Original-From: Daniel Roe Content-Type: multipart/alternative; boundary=001a11c36e1cf1c62504ee0e7845 Date: Sat, 21 Dec 2013 10:10:32 -0700 MIME-Version: 1.0 Sent to CCL by: Daniel Roe [daniel.r.roe[a]gmail.com] --001a11c36e1cf1c62504ee0e7845 Content-Type: text/plain; charset=ISO-8859-1 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> > E-mail to subscribers: CHEMISTRY(_)ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or use> > > -- ------------------------- 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) --001a11c36e1cf1c62504ee0e7845 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

You can try the 'reduce' program from AmberT= ools.=A0
http://ambermd.org

-Dan

On Saturday, December 21, 2= 013, 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. Ro= e, PhD
Department of Medicinal Chemistry
University of Utah
30 Sou= th 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.ed= u/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
--001a11c36e1cf1c62504ee0e7845--