From owner-chemistry@ccl.net Tue Mar 13 04:49:01 2007 From: "Orlin Blajiev Orlin.Blajiev[-]vub.ac.be" To: CCL Subject: CCL: Vibrational analysis in Gamess Message-Id: <-33784-070313044738-24401-8/uBRLEnlTCrS7r2KxhNfA---server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Mar 2007 09:47:02 +0100 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [Orlin.Blajiev .. vub.ac.be] Hi, I have some question about the vibrational analysis in Gamess. I have optimized geometry with another program and used it as input in Gamess with the STPT option on. I got the messages that * * * WARNING, MODE 1 HAS BEEN CHOSEN AS A VIBRATION WHILE MODE 7 IS ASSUMED TO BE A TRANSLATION/ROTATION. PLEASE VERIFY THE PROGRAM'S DECISION MANUALLY! and I am not sure what is this about. Second thing is that I do not see any negative frequencies in the output, but I also got a message 5 IMAGINARY FREQUENCY VIBRATION(S) IS(ARE) EXCLUDED FROM THE FOLLOWING THERMOCHEMICAL ANALYSIS. which are exactly the frequencies appearing in the WARNING above. I will appreciate any help. Best regards, Orlin -- ECASIA '07 will take place in Brussels > From 9th to 14th September 2007 http://www.ecasia07.be/ Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Tue Mar 13 15:01:04 2007 From: "sabri alkis alkis(!)ufl.edu" To: CCL Subject: CCL: sutton-chen potential DLPOLY Message-Id: <-33785-070313145954-10930-BiL21x1fDol12XcdN5tYxQ[*]server.ccl.net> X-Original-From: "sabri alkis" Date: Tue, 13 Mar 2007 14:59:50 -0400 Sent to CCL by: "sabri alkis" [alkis|ufl.edu] Hi everyone, I am trying to explain the Ag-Ag interactions with DLPOLY program. I found a L-J potential from literature. It gives good agreement with the experimental findings. Do I have to use sutton-chen potential or is it OK to explain metal-metal interactions with the L-J potential? How do we describe the Sutton-chen potential in a FIELD file? Is it by default? Do we have to explain all the metal-metal interactions with Sutton-Chen? What is the advantage of this potential? Is it also OK to explain the metal-metal interactions with UFF potential? Does anybody have an idea? Best wishes and thanks.. From owner-chemistry@ccl.net Tue Mar 13 15:55:03 2007 From: "Xun Li lixun_-_mail.sioc.ac.cn" To: CCL Subject: CCL: Where do Ludi fragment libraries in Discovery Studio come from? Message-Id: <-33786-070313100153-9409-i9RZM/+66KUIOqYenAwodQ]-[server.ccl.net> X-Original-From: "Xun Li" Date: Tue, 13 Mar 2007 10:01:50 -0400 Sent to CCL by: "Xun Li" [lixun],[mail.sioc.ac.cn] Hello, everyone! Would anyone please tell me where Ludi fragment libraries in Discovery Studio come from? Are they generated with some compound databases? Best regards, Xun Li From owner-chemistry@ccl.net Tue Mar 13 16:14:00 2007 From: "Prema latha Mallipeddi plmallip~!~mail.uh.edu" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33787-070313161102-22114-Sn+hYpE3sXTOKeEMHncZvg:_:server.ccl.net> X-Original-From: "Prema latha Mallipeddi" Date: Tue, 13 Mar 2007 16:10:58 -0400 Sent to CCL by: "Prema latha Mallipeddi" [plmallip++mail.uh.edu] Can anyone help me find a "Vi command" or an "Text editing idea"; i need to rename duplicate names repeating in an SDF file with chemical compounds. I would have used cerius2 or catalyst, but these platforms aren't accepting SD files with morethan 4000 compounds and some of my SD files have more than 20000 compounds (Splitting the SDfile doesn't serve my purpose) Thanks & regards, Latha. From owner-chemistry@ccl.net Tue Mar 13 19:21:01 2007 From: "Jeff Nauss jnauss{:}accelrys.com" To: CCL Subject: CCL: Where do Ludi fragment libraries in Discovery Studio come from? Message-Id: <-33788-070313191829-12711-F1WiSuggyjI6krYwNtN1wg]=[server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Tue, 13 Mar 2007 16:18:17 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss!=!accelrys.com] > Sent to CCL by: "Xun Li" [lixun],[mail.sioc.ac.cn] > Hello, everyone! > > Would anyone please tell me where Ludi fragment libraries in > Discovery Studio come from? Are they generated with some compound databases? There are three default Ludi fragment libraries when using the receptor mode in Discovery Studio. The default Accelrys fragment library was derived from the original Hans Bohm library in the original Ludi implementation. The intent was that these fragments are small organics that medicinal chemists and synthetic chemists would know how to connect them together in a synthetic pathway. The Organics and Peptide Fragments libraries come from the old Cerius2 fragment libraries used to build molecules. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Tue Mar 13 20:34:00 2007 From: "Wolf-D. Ihlenfeldt wdi^xemistry.com" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33789-070313202740-7303-Uj266oTDbnzVBMa5T1DEyw~~server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Mar 2007 19:27:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi]|[xemistry.com] Latha, this can easily be achieved with a short CACTVS script (CACTVS is free for academic use). Please send me some sample data. W. D. Ihlenfeldt Xemistry GmbH wdi!A!xemistry.com > -----Original Message----- > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] > Sent: Tuesday, March 13, 2007 4:11 PM > To: Ihlenfeldt, W.d. > Subject: CCL: Renaming Stereomers in SDF file > > > Sent to CCL by: "Prema latha Mallipeddi" > [plmallip++mail.uh.edu] Can anyone help me find a "Vi > command" or an "Text editing idea"; i need to rename > duplicate names repeating in an SDF file with chemical > compounds. I would have used cerius2 or catalyst, but these > platforms aren't accepting SD files with morethan 4000 > compounds and some of my SD files have more than 20000 > compounds (Splitting the SDfile doesn't serve my purpose) > > > Thanks & regards, > Latha. > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the !A! sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > >