From owner-chemistry@ccl.net Fri Jul 7 04:29:01 2006 From: "Raji Raji raji||anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: Counterpoise method in g03 Message-Id: <-32082-060707042722-15603-hSeqCdGRdtsQeb5E4Ov3nw[-]server.ccl.net> X-Original-From: "Raji Raji" Date: Fri, 7 Jul 2006 04:27:19 -0400 Sent to CCL by: "Raji Raji" [raji^anal.chem.tohoku.ac.jp] Dear CCL Members, In gaussian manual I have found the following model input for the Counterpoise method. In this, what does the numbers 1 and 2 represents (right side of the cartesian coordinates, and Counterpoise=2)? MP2/6-31G Counterpoise=2 Opt Counterpoise with Cartesian 0,1 1 0.00 0.00 0.92 1 9 0.17 0.00 2.73 2 1 0.77 0.00 3.43 2 9 0.00 0.00 0.00 1 Thanks in advance. Best Regards, Raji. From owner-chemistry@ccl.net Fri Jul 7 05:51:01 2006 From: "Renxiao Wang renxiao~~med.umich.edu" To: CCL Subject: CCL: The PDBbind database version 2005 is being released Message-Id: <-32083-060706055113-15260-lgz7wN/Ir5jVnLIpSYDduw++server.ccl.net> X-Original-From: "Renxiao Wang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 06 Jul 2006 04:26:26 -0400 Mime-Version: 1.0 Sent to CCL by: "Renxiao Wang" [renxiao : med.umich.edu] Dear researchers, We are glad to announce a new release of the PDBbind database, i.e. v.2005. The PDBbind database, publicly accessible at http://www.pdbbind.org/, is created to provide a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank (PDB). This new version has binding affinity data (Kd, Ki, & IC50) for over 2,700 protein-ligand complexes released by PDB before 01/01/2006. The PDBbind database is developed by Prof. Shaomeng Wang's group at the University of Michigan. All registered users may access this database using their current accounts. Other researchers are welcome to explore our web site through a demo account. Best regards, Renxiao Wang, Ph.D. Research Investigator University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Fri Jul 7 08:46:00 2006 From: "Sebastian H. Riedel sebastian.riedel]^[mail.uni-wuerzburg.de" To: CCL Subject: CCL:G: AW: G: Counterpoise method in g03 Message-Id: <-32084-060707083054-25373-IXLlLCPy2/egdQlEs+AXBg#%#server.ccl.net> X-Original-From: "Sebastian H. Riedel" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 7 Jul 2006 13:39:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Sebastian H. Riedel" [sebastian.riedel_-_mail.uni-wuerzburg.de] In the CP method you have to specify your fragments of the complex. The counterpoise keyword will specify how many fragments you have in the complex. Like the example of the Gaussian manual HBr + HF, optimization with counterpoise correction using ECP basis # hf/lanl2dz counterpoise=2 nosymm opt test 0 1 H -0.046866 0. 0.586860 1 Br -0.331864 0. -0.801000 1 F 0.396755 0. 2.739275 2 H 0.584835 0. 3.641534 2 You have specified two fragments: fragment 1 is HBr and fragment 2 is HF! In your example it means, fragment 1 is HF and fragment 2 is HF 1 0.00 0.00 0.92 1 9 0.17 0.00 2.73 2 1 0.77 0.00 3.43 2 9 0.00 0.00 0.00 1 Greetings S. Riedel -------------------------------------------- Dipl. Chem. Sebastian H. Riedel Workgroup Prof. Dr. M. Kaupp Institut für Anorganische Chemie University Würzburg Am Hubland D-97074 Würzburg, Germany Phone: +49-931-888-5495 E-mail: sebastian.riedel]~[mail.uni-wuerzburg.de www: http://www-anorganik.chemie.uni-wuerzburg.de/kaupp www: http://www.psichem.de -------------------------------------------- -----Ursprüngliche Nachricht----- Von: owner-chemistry]~[ccl.net [mailto:owner-chemistry]~[ccl.net] Gesendet: Freitag, 7. Juli 2006 13:11 An: Riedel, S Betreff: CCL:G: Counterpoise method in g03 Sent to CCL by: "Raji Raji" [raji^anal.chem.tohoku.ac.jp] Dear CCL Members, In gaussian manual I have found the following model input for the Counterpoise method. In this, what does the numbers 1 and 2 represents (right side of the cartesian coordinates, and Counterpoise=2)? MP2/6-31G Counterpoise=2 Opt Counterpoise with Cartesian 0,1 1 0.00 0.00 0.92 1 9 0.17 0.00 2.73 2 1 0.77 0.00 3.43 2 9 0.00 0.00 0.00 1 Thanks in advance. Best Regards, Raji.http://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 Jul 7 09:21:00 2006 From: "Sergio Emanuel Galembeck segalemb|*|usp.br" To: CCL Subject: CCL:G: Counterpoise method in g03 Message-Id: <-32085-060707084120-27759-Oa3FgK2BgJramveFTF6Efw],[server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 07 Jul 2006 09:40:51 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb a usp.br] Dear Raji, counterpoise=2 means this system is composed by two molecules, or HF---HF. The numbers on the right means that this atom belongs to the molecule 1 or 2. Hope this help you, Sergio Galembeck Citando "Raji Raji raji||anal.chem.tohoku.ac.jp" : > Sent to CCL by: "Raji Raji" [raji^anal.chem.tohoku.ac.jp] > > Dear CCL Members, > In gaussian manual I have found the following model input for the > Counterpoise method. In this, what does the numbers 1 and 2 represents (right > side of the cartesian coordinates, and Counterpoise=2)? > > > MP2/6-31G Counterpoise=2 Opt > > Counterpoise with Cartesian > > 0,1 > 1 0.00 0.00 0.92 1 > 9 0.17 0.00 2.73 2 > 1 0.77 0.00 3.43 2 > 9 0.00 0.00 0.00 1 > > Thanks in advance. > Best Regards, > Raji.> > > > From owner-chemistry@ccl.net Fri Jul 7 09:56:01 2006 From: "skull crossbones a_n_t_i_c_l_o_c_k:yahoo.com" To: CCL Subject: CCL: Prediction of Heteromeric interaction of membrane proteins Message-Id: <-32086-060707093926-13657-yaS/2tjI1lIOl7hYGCP5Qg(0)server.ccl.net> X-Original-From: "skull crossbones" Date: Fri, 7 Jul 2006 09:39:25 -0400 Sent to CCL by: "skull crossbones" [a_n_t_i_c_l_o_c_k[a]yahoo.com] Hello, Can anyone cite some literature references that point to Computational prediction of protein-protein interactions of Membrane proteins? I prefer to know about structure based methods like protein-protein docking etc. Though there are some references on prediction of Homomeric protein-protein associations, I didn't find any references for the prediction heteromeric association. Thanks in advance From owner-chemistry@ccl.net Fri Jul 7 11:57:00 2006 From: "Jeff Nauss jnauss.=.accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for August Message-Id: <-32087-060707015242-15090-U7cA5+ALvnw+PwnTYsWxEA=server.ccl.net> X-Original-From: Jeff Nauss Content-Type: multipart/alternative; boundary="=_alternative 001D3B9C882571A4_=" Date: Thu, 6 Jul 2006 22:52:08 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss=-=accelrys.com] This is a multipart message in MIME format. --=_alternative 001D3B9C882571A4_= Content-Type: text/plain; charset="US-ASCII" Accelrys Inc. are holding the following training workshops during August. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. SAN DIEGO, CA Introduction to Quantum Mechanics Modeling 9-10 August Accelrys GCG/SeqLab 30-31 August ONLINE TRAINING Introduction to Discovery Studio 22 Aug (9am PDT) Structure-Based Design in Discovery Studio 23 Aug (9am PDT) Protein Modeling in Discovery Studio 24 Aug (9am PDT) Simulations in Discovery Studio 25 Aug (9am PDT) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Questions regarding scheduling and content should be directed to workshops!^!accelrys.com -- 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/training --=_alternative 001D3B9C882571A4_= Content-Type: text/html; charset="US-ASCII"
Accelrys Inc. are holding the following training workshops during August.  These events are designed to help you get more value > from your Accelrys software, helping you to better accomplish your research goals.

Costs for the scheduled workshops are $500 per day for all customers.  For the on-line presentations, the price is $175 per three hour session for all customers.

SAN DIEGO, CA

Introduction to Quantum Mechanics Modeling     9-10 August
Accelrys GCG/SeqLab                           30-31 August

ONLINE TRAINING

Introduction to Discovery Studio               22 Aug (9am PDT)
Structure-Based Design in Discovery Studio     23 Aug (9am PDT)
Protein Modeling in Discovery Studio           24 Aug (9am PDT)
Simulations in Discovery Studio                25 Aug (9am PDT)

Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html.

Questions regarding scheduling and content should be directed to workshops!^!accelrys.com

--
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/training
 --=_alternative 001D3B9C882571A4_=-- From owner-chemistry@ccl.net Fri Jul 7 18:34:00 2006 From: "Pussana Hirunsit Pussana.Hirunsit|*|chemail.tamu.edu" To: CCL Subject: CCL:G: freezing atoms without Opt keyword Message-Id: <-32088-060706135644-29642-SlGYGGzN40/oWCtOOtG77g]^[server.ccl.net> X-Original-From: "Pussana Hirunsit" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 06 Jul 2006 12:12:52 -0500 MIME-Version: 1.0 Sent to CCL by: "Pussana Hirunsit" [Pussana.Hirunsit|chemail.tamu.edu] Dear All, I'm using Gaussian program to simulate proton transport in water clusters. I have fixed the coordinate of 6 water molecules(atom 1- 18) using keyword Opt=Z-Matrix. I also fix the distance between atom 20 and 23 and scan the distance between atom 25 and 23. My problem is I want the program to scan without optimization but if I don't use the keyword Opt=Z-Matrix, I can't freez atom 1-18 coordinate. Could you suggest me how to freez atoms' coordinate and scan without performing optimization (only SCF calculation)? The following is the input file. Thank you for your help. Best regards, Pussana Graudate Student Texas A&M University %chk=Scan_optZ_H14_5WGs.chk %mem=6MW %nproc=1 #p opt=z-matrix b3pw91/6-311++g(d,p) Scan H = 14.5, 6 fixed water Gaussian structure 1 1 O 0 A1 B1 C1 H 0 A2 B2 C2 H 0 A3 B3 C3 H 0 A4 B4 C4 O 0 A5 B5 C5 H 0 A6 B6 C6 H 0 A7 B7 C7 O 0 A8 B8 C8 H 0 A9 B9 C9 H 0 A10 B10 C10 O 0 A11 B11 C11 H 0 A12 B12 C12 H 0 A13 B13 C13 O 0 A14 B14 C14 H 0 A15 B15 C15 H 0 A16 B16 C16 O 0 A17 B17 C17 H 0 A18 B18 C18 H 14 E18 11 F17 1 D16 O 1 E19 5 F18 8 D17 H 20 E20 1 F19 5 D18 H 14 E21 11 F20 1 D19 O 20 E22 1 F21 5 D20 H 23 E23 5 F22 1 D21 H 23 E24 5 F23 1 D22 Variables: E18 1.38148229 E19 1.81948165 E20 0.95988000 E21 1.39818591 E23 0.97798322 E24 0.97821505 S 20 0.05 F17 92.29566127 F18 70.24991784 F19 81.22425202 F20 138.85801687 F21 103.16443835 F22 97.04460806 F23 129.70631822 D16 -28.25795916 D17 82.28508273 D18 -103.96750943 D19 -26.55081241 D20 -17.82012221 D21 171.42266725 D22 43.01697243 Constants: E22 2.38650760 A1 6.33352090 B1 -11.50135061 C1 -6.95376155 A2 5.92310099 B2 -11.59441427 C2 -7.81646907 A3 5.60910855 B3 -11.56976895 C3 -6.32773016 A4 5.27412536 B4 -8.92834151 C4 -6.11951656 A5 5.31057625 B5 -8.41595770 C5 -6.93038263 A6 5.45036168 B6 -7.51065384 C6 -6.64358204 A7 4.48628050 B7 -6.22853083 C7 -6.76203509 A8 4.95570918 B8 -5.39152723 C8 -6.78280310 A9 5.52568502 B9 -5.40959897 C9 -6.01068227 A10 5.76195214 B10 -12.96823713 C10 -3.85303503 A11 4.89351810 B11 -12.81302383 C11 -4.23132163 A12 4.81608461 B12 -11.85786920 C12 -4.28657840 A13 4.08182602 B13 -10.09144478 C13 -5.37812171 A14 4.56046487 B14 -10.17169968 C14 -4.54997099 A15 4.52252181 B15 -9.29642674 C15 -4.15776287 A16 3.42247562 B16 -7.16258216 C16 -4.20789650 A17 4.32392982 B17 -7.48410785 C17 -4.13460818 A18 4.80168447 B18 -6.77899183 C18 -3.69196669