From owner-chemistry@ccl.net Mon Dec 23 01:58:01 2013 From: "Rajeev Gangal rajeev.gangal],[gmail.com" To: CCL Subject: CCL: Tools to add hydrogens to ligands Message-Id: <-49476-131222020336-9761-H/eBGTQl/fxXe3WUD4zPsg[a]server.ccl.net> X-Original-From: Rajeev Gangal Content-Type: multipart/alternative; boundary=047d7b5d58a2cc5c2b04ee1a1b40 Date: Sun, 22 Dec 2013 12:33:29 +0530 MIME-Version: 1.0 Sent to CCL by: Rajeev Gangal [rajeev.gangal^^^gmail.com] --047d7b5d58a2cc5c2b04ee1a1b40 Content-Type: text/plain; charset=ISO-8859-1 Try http://www.tcd.uni-konstanz.de/research/spores.php On Sat, Dec 21, 2013 at 10:40 PM, Daniel Roe daniel.r.roe-x-gmail.com < owner-chemistry%%ccl.net> wrote: > 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) > --047d7b5d58a2cc5c2b04ee1a1b40 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Try http://www.tcd.uni-konstanz.de/research/spores.php


On Sat, Dec 21,= 2013 at 10:40 PM, Daniel Roe d= aniel.r.roe-x-gmail.com <owner-chemistry%%ccl.net> = wrote:
Hi,

You can try the '= reduce' program from AmberTools.=A0

-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



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^_^ccl.net or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST^_^ccl.net or use
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--
-------------------------
Daniel R. Roe, PhD
Department o= f 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)

--047d7b5d58a2cc5c2b04ee1a1b40-- From owner-chemistry@ccl.net Mon Dec 23 02:33:00 2013 From: "Radoslaw Kaminski rkaminski.rk*|*gmail.com" To: CCL Subject: CCL: Interpretation of TDDFT results Message-Id: <-49477-131223023122-25012-TDW8DeLmGFL+B04fAPCcJA]^[server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Mon, 23 Dec 2013 02:31:20 -0500 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]*[gmail.com] Dear All, I would like to ask a question regarding the practical interpretation of TDDFT results. When I do the TDDFT calculation I get a set of computed transitions, allowed and forbidden (e.g. S0 state -> T1 state). Later, in the output of various programs, there are shown as mixtures of some 'orbital transitions', with some coefficients. For example ADF prints out: 9: 405a -> 408a 0.9449 9: 406a -> 409a 0.0464 9: 400a -> 407a 0.0038 9: 401a -> 407a 0.0027 9: 405a -> 409a 0.0002 I was looking for a nice literature or tutorials how to practically interpret such results, unfortunately with no significant results. The thing I am a bit puzzled with is the relation of such 'mixed' transitions to the one-determinant approximation, which is used in the practical implementation of the DFT method. The S0 state has no unpaired electrons, T1 has two: one electron on former HOMO (now SOMO), and the other one on former LUMO (now other SOMO), and other excited configurations can be expressed in a similar way. Why then some of the computed transitions engage many orbitals with various contributions? What does it mean? Some nice tutorials or literature would be of a very much advantage for me. Thanks in advance. Best wishes, Radek From owner-chemistry@ccl.net Mon Dec 23 09:34:00 2013 From: "case case,,biomaps.rutgers.edu" To: CCL Subject: CCL: Tools to add hydrogens to ligands Message-Id: <-49478-131222090918-4951-cbLXTd1yHGWmheX/nmW3rA#server.ccl.net> X-Original-From: case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sun, 22 Dec 2013 09:09:15 -0500 Mime-Version: 1.0 Sent to CCL by: case [case{=}biomaps.rutgers.edu] On Sat, Dec 21, 2013, Daniel Roe daniel.r.roe-x-gmail.com wrote: > > You can try the 'reduce' program from AmberTools. > http://ambermd.org Just a clarification: the main author of reduce is J. Michael Word, and the main distribution site is http://kinemage.biochem.duke.edu/software/reduce.php. AmberTools just redistributes this as a convenience to our users. ...dave case From owner-chemistry@ccl.net Mon Dec 23 15:29:00 2013 From: "Fedor Goumans goumans%scm.com" To: CCL Subject: CCL: Interpretation of TDDFT results Message-Id: <-49479-131223152425-26938-gckD6xZjvny/y/GQs9Dd1g ~ server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Dec 2013 21:24:19 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans,+,scm.com] Dear Radek, Perhaps the Annual Reviews paper by Casida and Huix-Rotllant is instructive. Paragraph 2.2 describes excitations in a two-electron two-orbital system. http://www.annualreviews.org/doi/abs/10.1146/annurev-physchem-032511-143803 Best wishes, Fedor On 12/23/2013 8:31 AM, Radoslaw Kaminski rkaminski.rk*|*gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]*[gmail.com] > Dear All, > > I would like to ask a question regarding the practical interpretation of TDDFT results. When I do the TDDFT calculation I get a set of computed transitions, allowed and forbidden (e.g. S0 state -> T1 state). Later, in the output of various programs, there are shown as mixtures of some 'orbital transitions', with some coefficients. For example ADF prints out: > > 9: 405a -> 408a 0.9449 > 9: 406a -> 409a 0.0464 > 9: 400a -> 407a 0.0038 > 9: 401a -> 407a 0.0027 > 9: 405a -> 409a 0.0002 > > I was looking for a nice literature or tutorials how to practically interpret such results, unfortunately with no significant results. The thing I am a bit puzzled with is the relation of such 'mixed' transitions to the one-determinant approximation, which is used in the practical implementation of the DFT method. The S0 state has no unpaired electrons, T1 has two: one electron on former HOMO (now SOMO), and the other one on former LUMO (now other SOMO), and other excited configurations can be expressed in a similar way. Why then some of the computed transitions engage many orbitals with various contributions? What does it mean? Some nice tutorials or literature would be of a very much advantage for me. > > Thanks in advance. > > Best wishes, > > Radek> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans]*[scm.com http://www.scm.com