From owner-chemistry@ccl.net Sat Dec 21 07:15:00 2013 From: "Bin Sun sunbinxod{:}gmail.com" To: CCL Subject: CCL: Tools to add hydrogens to ligands Message-Id: <-49471-131221050202-8083-pKOSwMJQ8w/jzq/xZm2oZA%a%server.ccl.net> X-Original-From: Bin Sun Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 21 Dec 2013 18:01:57 +0800 MIME-Version: 1.0 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 From owner-chemistry@ccl.net Sat Dec 21 12:05:01 2013 From: "zvitnik zvitnik{:}chem.bg.ac.rs" To: CCL Subject: CCL:G: Fw: CCL: error termination via lnk1e in c:\G09w\1607.exe Message-Id: <-49472-131221111524-15145-VUMb844ovaCW3nzN6lq6qg a server.ccl.net> X-Original-From: zvitnik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sat, 21 Dec 2013 17:15:16 +0100 MIME-Version: 1.0 Sent to CCL by: zvitnik [zvitnik|a|chem.bg.ac.rs] Mahnaz, A few months ago I encountered a similar problem. NBO 3.1 from Gaussian, in situations when the basis set with diffuse functions was applied to highly delocalized system is not able to properly assign the electronic density of individual bonds according to Lewis theory. The only solution is to remove the diffuse functions from the basis set or to try some newer version of NBO program. Best regards, Zeljko On 2013-12-20 23:43, shanawersi shanawersi()upatras.gr wrote: > I think in order to visualize NBOs, there is no need to save it in > the checkpoint file. All required results will be written in output > file using pop=(nbo,full) instead of savenbos. In addition to this > you > should also use opt=tight instead of opt for tight convergence > criteria. I hope this will work. Good luck :). > > S. Niaz, Greece. > > On 2013-12-20 18:57, mahnaz ghiasi mahnaz271163],[yahoo.com wrote: > >> Dear shanawersi >> shanawersi >> Route >> section: # opt freq=raman b3lyp/6-311++g(d,p) pop=(nbo,savenbo) >> geom=connectivity >> >> On Friday, December 20, 2013 4:56 PM, shanawersi >> shanawersi~!~upatras.gr wrote: >> >> Mahnaz, you should be more specific in this case (NBOs)!!! Its >> better if you will provide some more details such as keywords you used >> in input and last part of output file etc. >> S. Niaz >> >> On 2013-12-20 12:25, mahnaz gh mahnaz271163:yahoo.com wrote: >> Sent to CCL by: "mahnaz gh" [mahnaz271163[-]yahoo.com] >> Hi there >> I ran an input in G09 and after 4 hours, the link died due to the >> "error termination via lnk1e in c:G09w1607.exe". Would you please help >> me to solve this problem? >> regards -= This is automatically added to each message by the >> mailing script =-E-mail to subscribers: CHEMISTRY|a|ccl.net or use:[1] E-mail to >> administrators: CHEMISTRY-REQUEST|a|ccl.net or >> useSubscribe/Unsubscribe:Before posting, check wait time at: >> http://www.ccl.netConferences: [2] >> http://server.ccl.net/chemistry/announcements/conferences/ [3] Search >> Messages: >> http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt---1131079492-989901180-1387558647=:19483 >> [4] >> Content-Type: text/html; charset=iso-8859-1 >> Content-Transfer-Encoding: quoted-printable >> >> Hi there >> I ran an input in G09 and after 4 hours, the link died due to the >> "error termination via lnk1e in c:G09w1607.exe". Would you please help >> me to solve this problem? >> regards >> From owner-chemistry@ccl.net Sat Dec 21 15:25:00 2013 From: "Geoffrey Hutchison geoffh{:}pitt.edu" To: CCL Subject: CCL: Tools to add hydrogens to ligands Message-Id: <-49473-131221152420-19701-j8kt1egSn+HN11jh5UgsEw,+,server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 21 Dec 2013 15:24:14 -0500 Mime-Version: 1.0 (Mac OS X Mail 7.1 \(1827\)) 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 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 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-- From owner-chemistry@ccl.net Sat Dec 21 21:54:00 2013 From: "Radoslaw Kaminski rkaminski.rk]_[gmail.com" To: CCL Subject: CCL: Total density from unrestricted ADF calculations Message-Id: <-49475-131221215324-5284-0v9w3FncpZbswS+Htd4IlA[#]server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Sat, 21 Dec 2013 21:53:23 -0500 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk _ gmail.com] Dear All, I was trying to use ADF densf utility to compute the total density from my unrestricted calculations. I used the keyword: Density SCF This resulted in two CUB files, each with alpha and beta densities. Is there a way to compute one single grid with total density? Obviously I can sum those grids manually, but I would like to produce the total density grid at once. Thanks in advance, Regards Radek