From ccl@www.ccl.net Tue Jun 24 02:45:06 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id BAA05411; Tue, 24 Jun 1997 01:56:34 -0400 (EDT) Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by bedrock.ccl.net (8.8.3/950822.1) id BAA05653; Tue, 24 Jun 1997 01:56:33 -0400 (EDT) Received: by SECS.UCSC.EDU (MX V3.1C) id 11414; Mon, 23 Jun 1997 22:56:09 PDT Date: Mon, 23 Jun 1997 22:56:08 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Message-ID: <009B63B1.19E2B200.11414@SECS.UCSC.EDU> Subject: Postdoctoral Position in Computational Chemistry The Molecular Engineering Laboratory at the University of California, Santa Cruz announces two postdoctoral positions available immediately. The candidates should have a Ph.D. in chemistry with experience in computational chemistry, molecular modeling of organic structures. Experience in developing new programs using C, C++, for molecule manipulation and molecular interaction simulation, and ability to work in a team with others is essential. The research of this laboratory is aimed at automated molecular design of a variety of structures, including drugs and other organic molecules requiring rigorous engineering approaches. Potential candidates should send their curriculum vita and correspondence to: Professor Todd Wipke Molecular Engineering Laboratory Department of Chemistry University of California Santa Cruz, CA 95064 FAX 408-459-2397 (but address it clearly to Wipke) email wipke@moleng.ucsc.edu Please forward to potential candidates. From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Jun 24 08:54:41 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id HAA07042; Tue, 24 Jun 1997 07:45:48 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA15953; Tue, 24 Jun 97 13:45:44 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA08304; Tue, 24 Jun 97 13:42:25 +0200 X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Jun 1997 12:42:05 +0100 To: Shubin Liu , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:Global minimization Dear Shubin Liu, At 15:41 Uhr 20.06.1997, Shubin Liu wrote: >As geometrical optimization only gives a local minimal, I hope to find a >way, if possible, to achieve the global minimal for a molecule. At least, >I hope that some way to check if the optimized structure is a local or >global minimal is available somewhere. Any comments are welcome. Thanx. Try a look at: H. A. Scheraga (1996). "Recent developments in the theory of protein-folding - searching for the global energy minimum." Biophysical Chemistry 59(3) 329-339. A. H. G. Rinnooy Kan, C. G. E. Boender and G. Th. Timmer (1985). A Stochasitc Approach to Global Optimization. Computational Mathematical Programming. Berlin, Springer. 282-308. R. Abagyan and M. Totrov (1994). "Biased probability monte-carlo conformational searches and electrostatic calculations for peptides and proteins." Journal of Molecular Biology 235(3) 983-1002. Hans Bremermann (1970). "A Method of Unconstrained Global Optimization." Mathematical Biosciences 9 1-15. Eberhard von Kitzing (1992). Modeling DNA Structures: Molecular Mechanics and Molecular Dynamics. Methods in Enzymology. San Diego, Academic Press. 449-466. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From yubofan@guomai.sh.cn Tue Jun 24 10:45:11 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id KAA08708; Tue, 24 Jun 1997 10:12:43 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id XAA14778 for ; Tue, 24 Jun 1997 23:09:06 +0800 Message-Id: <199706241509.XAA14778@gm-email.guomai.sh.cn> From: "·ΆΣύ²¨" To: Subject: Want a program ot visualize electronic density contour. Date: Tue, 24 Jun 1997 22:06:53 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, ccl'er, I do some calculations on my PC by G94W. I want ot visualize the electric density contour. Which program can this job? A small one is preferred. Thanks Y. FAN From toukie@zui.unizh.ch Tue Jun 24 10:45:15 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA08593; Tue, 24 Jun 1997 10:00:10 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05512; Tue, 24 Jun 1997 15:59:04 +0200 Message-Id: <1.5.4.32.19970624140118.00668464@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Jun 1997 16:01:18 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: van der Waals radii for amino acids Cc: toukie@zui.unizh.ch Dear Colleagues; For a calculation I wish to perform, I require the van der Waals radii of each of the atoms (including hydrogen) in the 20 common amino acids. If anyone can recommend a published source of this information (or if anyone should happen to have this information as an e-mailable file), I would appreciate hearing from you. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From yubofan@guomai.sh.cn Tue Jun 24 10:45:20 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id KAA08711; Tue, 24 Jun 1997 10:12:50 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id XAA14782 for ; Tue, 24 Jun 1997 23:09:14 +0800 Message-Id: <199706241509.XAA14782@gm-email.guomai.sh.cn> From: "·ΆΣύ²¨" To: Subject: Why does G94W's SCF option make errors? Date: Tue, 24 Jun 1997 22:08:30 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, ccl'ers, I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I try "restart", a SCF option that I didn't use before. I kill the job after L502.exe had been running 4 cycles, then I put "restart" after "SCF=". I ran the calculation again. L502.exe did 2 cycles and the result was gotten. Again I did the job from the very original start. After 6 cycles had been done, another result was gotten. I list them below: :With SCF=(save, restart) Convergence on energy, delta-E=1.12D-05 SCF Done: E(RB-LYP) = -692.644057005 A.U. after 2 cycles Convg = 0.2054D-03 -V/T = 2.0090 S**2 = 0.0000 KE= 6.864357999909D+02 PE=-3.864671343753D+03 EE= 1.355127785196D+03 :With SCF=save SCF Done: E(RB-LYP) = -692.644408415 A.U. after 6 cycles Convg = 0.4070D-05 -V/T = 2.0094 S**2 = 0.0000 KE= 6.861718246427D+02 PE=-3.864945652472D+03 EE= 1.355665717853D+03 Why do they have error I think it considerable great? Thanks a lot Y. FAN From ophira@keyscan.com Tue Jun 24 22:45:13 1997 Received: from mailnfs0.tiac.net for ophira@keyscan.com by www.ccl.net (8.8.3/950822.1) id VAA13004; Tue, 24 Jun 1997 21:59:23 -0400 (EDT) Received: from keyscan.tiac.net (keyscan.tiac.net [199.3.128.220]) by mailnfs0.tiac.net (8.8.0/) with SMTP id VAA02461 for ; Tue, 24 Jun 1997 21:59:25 -0400 (EDT) Received: by keyscan.tiac.net with Microsoft Mail id <01BC80EA.19D19740@keyscan.tiac.net>; Tue, 24 Jun 1997 22:01:00 -0400 Message-ID: <01BC80EA.19D19740@keyscan.tiac.net> From: OPHIRA AHARONSON To: "'CHEMISTRY@www.ccl.net'" Subject: unsubscribe Date: Tue, 24 Jun 1997 21:59:28 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit unsubscribe