From owner-chemistry@ccl.net Fri Sep 5 07:18:01 2014 From: "Grigoriy Zhurko gzhurko*o*chemcraftprog.com" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50475-140905004749-12362-XfCNa0qyYYX+FNPDl3S7wA(~)server.ccl.net> X-Original-From: "Grigoriy Zhurko" Date: Fri, 5 Sep 2014 00:47:48 -0400 Sent to CCL by: "Grigoriy Zhurko" [gzhurko(_)chemcraftprog.com] My program Chemcraft sometimes incorrectly identifies the bonds between atoms, in particular H-bonds. Where I can read more about algorithms of bond identification? From owner-chemistry@ccl.net Fri Sep 5 07:53:00 2014 From: "Barry Hardy barry.hardy\a/vtxmail.ch" To: CCL Subject: CCL: ToxBank public access open Message-Id: <-50476-140905025102-19493-F/VE7DwBkAJoQ93iOifhDQ-.-server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 05 Sep 2014 08:50:52 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]![vtxmail.ch] We are pleased to inform that we are commencing providing public acccess to the ToxBank Data Warehouse. Public access to the data warehouse may be requested using the form available at: http://www.toxbank.net/enquiries/request-data-warehouse-access Users may access protocols or data that have been made available within the ToxBank Data Warehouse. We also provide a request option to support the incorporation of your data, accompanied by access, security and license protections, including for confidential or open data. Tutorials on the use of the ToxBank resources are made available in the ToxBank Library at http://www.toxbank.net/tutorials best regards Barry Hardy as ToxBank Scientific Coordinator Douglas Connect GmbH Switzerland From owner-chemistry@ccl.net Fri Sep 5 10:47:00 2014 From: "Andy Wong andy.wong%a%monash.edu" To: CCL Subject: CCL:G: G09 Keyword: Freq Message-Id: <-50477-140905091025-15640-zqPgfuMhpMuKJf8sZD/mkA.:.server.ccl.net> X-Original-From: "Andy Wong" Date: Fri, 5 Sep 2014 09:10:23 -0400 Sent to CCL by: "Andy Wong" [andy.wong[-]monash.edu] I am trying to use the Freq=(anharmonic,readanharm) keyword with the command PT2Model=GVPT2 in Gaussian 09. However the log file says that this is not a recognised command. Any help is appreciated. Regards Andy Wong andy.wong]^[monash.edu From owner-chemistry@ccl.net Fri Sep 5 11:46:00 2014 From: "Jens Spanget-Larsen spanget_._ruc.dk" To: CCL Subject: CCL:G: G09 Keyword: Freq Message-Id: <-50478-140905114412-11443-3Nj2zZwvCfCCfgRczsR8PQ a server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 5 Sep 2014 15:40:35 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget===ruc.dk] Dear Andy: Application of Freq=(anharmonic,readanharm) may be quite tricky. I suggest you contact Fernando R. Clemente of Gaussian Technical Support (help.at.gaussian.com), he was very helpful when we had problems with this keyword/option in a recent investigation (Spanget-Larsen et al., Chemical Physics 389, 107-115 (2011)). Yours, Jens >--<   ------------------------------------------------------   JENS SPANGET-LARSEN         Office:      +45 4674 2710   Dept. of Science (NSM)      Fax:         +45 4674 3011   Roskilde University         Mobile:      +45 2320 6246   P.O.Box 260                 E-Mail:     spanget{:}ruc.dk   DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget   ------------------------------------------------------ -----Original Message----- > From: owner-chemistry+spanget==ruc.dk{:}ccl.net [mailto:owner-chemistry+spanget==ruc.dk{:}ccl.net] On Behalf Of Andy Wong andy.wong%a%monash.edu Sent: 5. september 2014 15:10 To: Jens Spanget-Larsen Subject: CCL:G: G09 Keyword: Freq Sent to CCL by: "Andy Wong" [andy.wong[-]monash.edu] I am trying to use the Freq=(anharmonic,readanharm) keyword with the command PT2Model=GVPT2 in Gaussian 09. However the log file says that this is not a recognised command. Any help is appreciated. Regards Andy Wong andy.wong\a/monash.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Sep 5 12:20:01 2014 From: "Abrash, Samuel sabrash{=}richmond.edu" To: CCL Subject: CCL:G: G09 Keyword: Freq Message-Id: <-50479-140905114601-12704-UpOvAv3pUx4OZIgXcZ0gZg~!~server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Sep 2014 15:45:54 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash]_[richmond.edu] Could you show your full command line? -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu!=!ccl.net [mailto:owner-chemistry+sabrash==richmond.edu!=!ccl.net] On Behalf Of Andy Wong andy.wong%a%monash.edu Sent: Friday, September 05, 2014 9:10 AM To: Abrash, Samuel Subject: CCL:G: G09 Keyword: Freq Sent to CCL by: "Andy Wong" [andy.wong[-]monash.edu] I am trying to use the Freq=(anharmonic,readanharm) keyword with the command PT2Model=GVPT2 in Gaussian 09. However the log file says that this is not a recognised command. Any help is appreciated. Regards Andy Wong andy.wong\a/monash.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Sep 5 13:40:00 2014 From: "Elaine Meng meng|a|cgl.ucsf.edu" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50480-140905132322-8257-+YFL24zOIgbH/PQSJeOB4A#%#server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 5 Sep 2014 13:23:14 -0400 Sent to CCL by: "Elaine Meng" [meng_-_cgl.ucsf.edu] Hi Grigoriy, Some programs just use a simple single distance cutoff between donor and acceptor heavy atoms, while others also use an angle cutoff. Probably you would have to look at the manual of each program to find the details. I work on UCSF Chimera, and its method is relatively complicated in that there are many different cutoffs: it uses different distance and angle cutoffs depending on the atom types of the donor and acceptor. It uses certain values for each combination of types as observed in a set of high-resolution small molecule crystal structures. Then to those values, the user can specify an extra distance tolerance and angle tolerance, since the criteria from the survey are very strict. Details here: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco