From jmuilu@joyke7.joensuu.fi Tue Nov 15 03:26:40 1994 Received: from joyx.joensuu.fi for jmuilu@joyke7.joensuu.fi by www.ccl.net (8.6.9/930601.1506) id CAA13108; Tue, 15 Nov 1994 02:52:25 -0500 Received: by joyx.joensuu.fi (5.57/Ultrix3.0-C) id AA18058; Tue, 15 Nov 94 09:46:20 +0200 Received: by joyke7.joensuu.fi (NX5.67d/NeXT-2.0) id AA07721; Tue, 15 Nov 94 09:51:53 +0200 Date: Tue, 15 Nov 94 09:51:53 +0200 From: jmuilu@joyke7.joensuu.fi (Juha Muilu) Message-Id: <9411150751.AA07721@joyke7.joensuu.fi> Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: Tony Dyson , CHEMISTRY@ccl.net Subject: Re: CCL:Gaussian-92 system performance numbers? Tony, I have compiled some g92 timings from several sources. Here is the summary: Computer Proc MHz Nproc LP 178 G92 Version Mflops min -------------------------------------------------------------------- SGI Indigo/32Mb R4000 50/100 1 16 111 RevC.3 SGI Indigo/32Mb R4400 75/150 1 24 80 RevC.3 IBM RS6000 590/256MB Power2 66 1 132(* 20 RevB IBM RS6000 590/256MB Power2 66 1 132(* 17 RevG3 IBM RS6000 380/32MB Power2 57 1 50 45 RevB IBM RS6000 370 Power 62 1 26 57 IBM RS6000 550 Power 42 1 26 61 IBM RS6000 540 Power 30 1 19 83 IBM RS6000 32H/16MB Power 25 1 12 134 RevB DEC 3000 AXP 800/Unix Alpha 200 1 44 RevE.2 DEC 3000 300 Alpha 150 1 144 DEC 3000 500X Alpha 200 1 59 DEC 3000 AXP 400/VMS Alpha 133 1 26 90 RevG.2 Cray X-MP EA/432 117 1 66 17 CRAY C90 8/256 ~250 1 4.25 RevC.3 CRAY C90 8/256(incore) ~250 1 1.5 RevC.3 CRAY YMP EL 34 1 39 Convex C3840 37 1 39 Convex C3840 37 2 39 *) with VAST-preprocessor ? Nproc) Number of processors used. LP ) Linpack DP (100x100). 178) Test 178 from g92 test suite. Elapsed wall clock time in minutes. (Should be close to CPU+system time, when Nproc = 1) Number of basis functions: 300 SCF iterations: 8 Input stream: %mem=2000000 #P RHF/6-31G** scf=direct test pop=npa prop=fit Gaussian 92 Test Job 178: TATB rhf/6-31g**//hf/6-31g** Energy should be -1006.2213391 ---------------- Best Regards, Juha Muilu Department of Chemistry,University of Joensuu,P.O. Box 111 80101 Joensuu,FINLAND Email:Juha.Muilu@joensuu.fi (NeXT mail ok) Phone:358-73-1513312,Fax:358-73-1513390 From rachelle@picard.niehs.nih.gov Tue Nov 15 10:26:48 1994 Received: from kamakazi.niehs.nih.gov for rachelle@picard.niehs.nih.gov by www.ccl.net (8.6.9/930601.1506) id JAA15752; Tue, 15 Nov 1994 09:37:44 -0500 Received: from picard.niehs.nih.gov by kamakazi.niehs.nih.gov via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@ccl.net id AA04622; Tue, 15 Nov 94 09:32:13 -0500 Received: by picard.niehs.nih.gov (931110.SGI/930416.SGI.AUTO) for @kamakazi.niehs.nih.gov:CHEMISTRY@ccl.net id AA01889; Tue, 15 Nov 94 09:37:33 -0500 Date: Tue, 15 Nov 94 09:37:33 -0500 From: rachelle@picard.niehs.nih.gov (Rachelle J. Bienstock) Message-Id: <9411151437.AA01889@picard.niehs.nih.gov> To: CHEMISTRY@ccl.net Subject: Zn potentials in biomolecular modeling.... HI- I would like to know what people have been using for Zn potentials in modeling Zn containing proteins. I have noticed that none of the Biosym forcefields nor AMBER contains potentials for Zn. If people develop their own potentials for these purposes, I would appreciate knowing how they then place them in the AMBER or any of the BIOSYM forcefields to use for molecular dynamics. Also, if someone knows whether any other forcefields which are suited for proteins contain potentials for Zn, I would appreciate knowing... i.e. such as Molecular Simulations, MacroModel or GROMOS... Thanks, Rachelle ##### (o o) +------------------------oooO---(__)---Oooo----------------------------+ | | | Dr. Rachelle Bienstock INTERNET :rachelle@picard.niehs.nih.gov | | National Institute of | | Environmental Health Sciences | | P.O. Box 12233 Mail Drop 10-03 Telephone : 919-541-3397 | | Research Triangle Park, NC 27709 Fax : 919-541-1578 | +----------------------------------------------------------------------+ || || (__) (__) From ernst@bkfug.kfunigraz.ac.at Tue Nov 15 12:26:50 1994 Received: from bkfug.kfunigraz.ac.at for ernst@bkfug.kfunigraz.ac.at by www.ccl.net (8.6.9/930601.1506) id LAA17645; Tue, 15 Nov 1994 11:27:40 -0500 Received: by bkfug.kfunigraz.ac.at (MX V4.0-1 AXP) id 1; Tue, 15 Nov 1994 17:28:05 --0100 Date: Tue, 15 Nov 1994 17:28:04 --0100 From: MARGOT To: chemistry@ccl.net Message-ID: <00987836.B69243C2.1@bkfug.kfunigraz.ac.at> Subject: R. Bader's Program Hi, I'm looking for information on the program written by Richard Bader for charge-density partitioning. My group here in Graz had a copy of it before my time, and it got lost due to a disk crash. We'd like to replace it; any pointers, any way to contact the author(s) would be much appreciated. Thanks, margot From DEPAZ@vm1.sdi.uam.es Tue Nov 15 12:33:12 1994 Received: from vm1.sdi.uam.es for DEPAZ@vm1.sdi.uam.es by www.ccl.net (8.6.9/930601.1506) id LAA17622; Tue, 15 Nov 1994 11:27:22 -0500 Message-Id: <199411151627.LAA17622@www.ccl.net> Received: from vm1.sdi.uam.es by vm1.sdi.uam.es (IBM VM SMTP V2R2) with BSMTP id 2123; Tue, 15 Nov 94 17:26:07 HOE Received: from vm1.sdi.uam.es (DEPAZ) by vm1.sdi.uam.es (Mailer R2.08) with BSMTP id 4940; Tue, 15 Nov 94 17:26:05 HOE Date: Tue, 15 Nov 94 17:22:49 HOE From: "Dr. Jose Luis Garcia de Paz" Organization: Native address: Subject: shareware version of Mopac for osf/1 To: CCL List Dear CCL'ers, Can anybody tell me where can I get a shareware version of MOPAC suitable to run in DEC OSF/1 operating system?. Does it include easy instructions to compile, for non expert users?. I have access to internet. Thank you very much. Regards, Jose Dr. Jose Luis Garcia de Paz (34) (1) 3974957. FAX (34) (1) 3974512. Departamento de Quimica Fisica Aplicada. FACULTAD DE CIENCIAS, C-XIV-602. Universidad Autonoma de MAdrid. 28049-Madrid (Spain). From rs0thp@rohmhaas.com Tue Nov 15 15:27:20 1994 Received: from monte.br.rohmhaas.com for rs0thp@rohmhaas.com by www.ccl.net (8.6.9/930601.1506) id PAA21402; Tue, 15 Nov 1994 15:11:59 -0500 Received: by monte.br.rohmhaas.com (AIX 3.2/UCB 5.64/4.03) id AA20436; Tue, 15 Nov 1994 15:05:19 -0500 From: rs0thp@rohmhaas.com (Dr. Tom Pierce) Message-Id: <9411152005.AA20436@monte.br.rohmhaas.com> Subject: mol file conversions to XYZ? To: chemistry@ccl.net Date: Tue, 15 Nov 1994 15:05:18 -0500 (EST) Cc: rdruker@rohmhaas.com X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 419 Dear CCLers, Is there any software free or commercial that converts mol file format connection tables (from the NCI database) to approximate XYZ coordinates? Thanks. I will summarize and repost if you send responses to my email address THPierce@RohmHaas.Com. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." From BILLINGS@UConnVM.UConn.Edu Tue Nov 15 16:26:56 1994 Received: from phem3 for BILLINGS@UConnVM.UConn.Edu by www.ccl.net (8.6.9/930601.1506) id PAA22684; Tue, 15 Nov 1994 15:51:39 -0500 Received: from UCONNVM.UCONN.EDU (MAILER@UCONNVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HJIIAYAGPC8YEEUJ@phem3.acs.ohio-state.edu>; Tue, 15 Nov 1994 15:51:35 EST Received: from UConnVM.UConn.Edu (BILLINGS) by UCONNVM.UCONN.EDU (Mailer R2.08 R208004) with BSMTP id 8931; Tue, 15 Nov 94 14:43:21 EST Date: Tue, 15 Nov 1994 14:40:19 -0500 (EST) From: Eric Billings Subject: MOPAC Cu Complex questions To: CHEMISTRY@ccl.net Message-id: <01HJIIAYAQCI8YEEUJ@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Hello fellow netters: We have been using MOPAC (AM1 hamiltonian) to generate partial charges on a tetradentate dinegative ligand that has a metal binding site and a separate protonation site (an amine). The ligand has one plane of symmetry. We have used sparkles to mimic the charge polarization of the metal center since we have been unable to locate parameters for copper (I and II). /CH2-C=O + CH2-NH O H3N \ / \ / C Cu(I/II) H3C / \ / \ CH2-NH O \CH2-C=O We have two questions: 1. Are there MOPAC parameters for Cu I and II available ? 2. Can anyone help explain why MOPAC is able to converge in three of the four cases below - but fail on the fourth. We have found the following: 1. When the ++ sparkle is used, and the protonation site is protonated (-NH3+) the set of partial charges obtained reflects the symmetry of the ligand. (Total molecular charge: +1) 2. When the ++ sparkle is used, and the protonation site is unprotonated (-NH2) the set of partial charges obtained reflects the symmetry of the ligand. (Total molecular charge: 0) 3.When a + sparkle is used, and the protonation site is protonated, a set of charges is obtained which also properly reflects ligand symmetry. (Total molecular charge: 0) 4. However, when a + sparkle and no protonation is used, MOPAC cannot converge with a total molecular charge: -1. However, if CHARGE=-0.999 is used, convergence is achieved with questionable results. Specifically, the partial charges do not reflect the symmetry of the molecule. This result appears to be chemically unreasonable. In addition, the assymetry of the partial charges in (4) can be reversed simply by rotating the -NH2 group around its C-N axis. We would appreciate suggestions about any fixes for this problem, or discussion about the result. Please respond to me directly and I'll summarize if folks are interested. We've included the input file for the difficult case below. Thanks !!! - Eric Eric Billings Biophysics Grad Student UCONN Billings@uconnvm.uconn.edu ------------------------------------------------------------------- Here's the file that converges with CHARGE=-0.999 (but not -1) and produces the asymmetric charges. ------------------------------------------------------------------- GRAPH UHF CHARGE=-0.999 AM1 1SCF INSIGHT generated AMPAC/MOPAC input file DATE: Fri Nov 4 15:19:28 1994 + 0.000000 0 0.000000 0 0.000000 0 0 0 0 O 3.945394 0 0.000000 0 0.000000 0 1 0 0 N 1.988805 0 63.980175 0 0.000000 0 1 2 0 C 1.243780 0 21.286814 0 11.840311 0 2 3 1 C 2.483390 0 95.464783 0 177.089172 0 3 1 4 C 2.741488 0 155.718201 0 172.258453 0 1 3 4 O 2.069859 0 98.706131 0 -90.481331 0 1 3 4 O 1.959568 0 83.935295 0 97.237152 0 1 3 7 O 1.954638 0 172.158951 0 76.167824 0 1 3 8 O 1.222477 0 123.999367 0 178.865356 0 6 9 1 N 1.998371 0 95.456062 0 166.698486 0 1 3 8 N 1.512800 0 138.539734 0 -136.269485 0 5 3 1 C 1.476681 0 104.733261 0 -164.992844 0 3 1 11 C 1.468735 0 117.143456 0 -38.470036 0 3 1 11 C 1.529775 0 112.715981 0 -70.285004 0 5 14 3 C 1.519738 0 116.683731 0 -1.443380 0 6 9 1 C 1.516491 0 112.850174 0 59.862339 0 5 14 3 H 0.847857 0 105.924355 0 85.132477 0 3 1 11 H 0.852142 0 104.861160 0 -84.707642 0 11 1 3 H 0.971031 0 110.465836 0 -54.648548 0 12 5 14 H 0.898043 0 112.369568 0 -179.796890 0 12 5 14 H 0.939738 0 109.942955 0 74.964302 0 13 3 1 H 0.869576 0 109.047089 0 -157.552032 0 13 3 1 H 0.983221 0 107.203888 0 -61.799381 0 14 3 1 H 0.912557 0 110.428726 0 176.152573 0 14 3 1 H 0.931023 0 109.966446 0 -49.515186 0 15 5 14 H 0.900946 0 110.653557 0 -169.862305 0 15 5 14 H 0.944812 0 109.929031 0 -90.911400 0 16 11 1 H 0.881151 0 109.577477 0 148.162247 0 16 11 1 H 0.930954 0 112.317932 0 -61.163052 0 17 5 14 H 0.964762 0 109.814117 0 55.678158 0 17 5 14 H 1.001573 0 109.777176 0 175.788788 0 17 5 14 H 0.942113 0 106.874374 0 -179.980927 0 7 1 3 H 1.210611 0 104.268616 0 69.931961 0 7 1 3 ------------------------------------------------------------------- From stoutepf@chemsci1.es.dupont.com Tue Nov 15 18:26:51 1994 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.9/930601.1506) id RAA24791; Tue, 15 Nov 1994 17:57:29 -0500 Received: by gatekeeper.es.dupont.com; id AA18878; Tue, 15 Nov 94 17:57:17 -0500 Received: from [158.117.153.76] by chemsci1.es.dupont.com (4.1/SMI-4.1) id AA24113; Tue, 15 Nov 94 17:54:17 EST Message-Id: <9411152254.AA24113@chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Tue, 15 Nov 1994 17:57:11 -0500 To: chemistry@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Structural comparison of coagulation cascade serine proteases Cc: hodgecn@lldmpc.dnet.dupont.com (Nick Hodge) Dear Netters, My request may not be really computational in nature. I am looking for recent papers that deal with: 1) a structural comparison of serine proteases in the coagulation cascade and/or: 2) homology modelling of those enzymes. Failing that references to structural comparisons or homology modelling of serine proteases in general would be highly appreciated. Thanks a million. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From lrbu00@xd88.kodak.com Tue Nov 15 19:26:51 1994 Received: from Kodak.COM for lrbu00@xd88.kodak.com by www.ccl.net (8.6.9/930601.1506) id TAA25447; Tue, 15 Nov 1994 19:15:08 -0500 From: Received: from euler.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA19087; Tue, 15 Nov 94 13:41:22 -0500 Reply-To: lrbu00@xd88.kodak.com Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.Kodak.COM:chemistry@ccl.net id AA24081; Tue, 15 Nov 94 12:28:25 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA15954; Tue, 15 Nov 1994 12:17:28 -0500 Date: Tue, 15 Nov 1994 12:17:28 -0500 Message-Id: <9411151217.ZM18000@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: Additional Gaussian Timings for TEST0178 Cc: Mckelvey@Kodak.COM Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: Several addenda for recent benchmarkings of Gaussian G3 and TEST0178 SGI/R8000 16 Min (By Roberto Gomperts at SGI) IBM 590/pwr2 17 Min (Kodak) IBM 390/pwr2 41 Min (Kodak; Same executable images as for 590/pwr2) 90 Mhz Pentium 600 Min (Kodak; Micronics mb with 512K cache and 32MB memory) Regards -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From tps@iris27.biosym.com Tue Nov 15 20:27:01 1994 Received: from bioc1.biosym.com for tps@iris27.biosym.com by www.ccl.net (8.6.9/930601.1506) id UAA25965; Tue, 15 Nov 1994 20:06:00 -0500 Received: from iris27.biosym.com by bioc1.biosym.com (5.64/0.0) id AA13590; Tue, 15 Nov 94 17:05:30 -0800 Received: by iris27.biosym.com (931110.SGI/930416.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA14590; Tue, 15 Nov 94 17:05:10 -0800 Date: Tue, 15 Nov 94 17:05:10 -0800 From: tps@iris27.biosym.com (Tom Stockfisch) Message-Id: <9411160105.AA14590@iris27.biosym.com> To: chemistry@ccl.net Subject: Re: Zn potentials in biomolecular modeling chelle@picard.niehs.nih.gov (Rachelle J. Bienstock) writes: > I would like to know what people have been using for Zn potentials in > modeling Zn containing proteins. I have noticed that none of the Biosym > forcefields nor AMBER contains potentials for Zn. The CFF93 force field released by the Potential Energy Functions Consortium at Biosym has parameters for Zn, as well as the metal ions Ca Cs Cu Fe K Li Mg Na Rb -- Tom Stockfisch, BIOSYM Technologies tps@biosym.com From lrbu00@xd88.kodak.com Tue Nov 15 21:26:53 1994 Received: from Kodak.COM for lrbu00@xd88.kodak.com by www.ccl.net (8.6.9/930601.1506) id UAA26244; Tue, 15 Nov 1994 20:49:42 -0500 From: Received: from euler.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA03694; Tue, 15 Nov 94 16:10:43 -0500 Reply-To: lrbu00@xd88.kodak.com Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.Kodak.COM:chemistry@ccl.net id AA24613; Tue, 15 Nov 94 16:05:27 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA17629; Tue, 15 Nov 1994 15:54:33 -0500 Date: Tue, 15 Nov 1994 15:54:33 -0500 Message-Id: <9411151554.ZM16091@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: Symposium on Semi-Empirical Theory Cc: McKelvey@Kodak.COM Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: ACS Symposium on Parameterisations in Semi-Empirical Theory Chicago ACS Meeting, August 20-24, 1995. Just to keep you up to date: Speakers: Walter Thiel, James Stewart, Karl Jug, Andreas Klamt, Michael Zerner, Andy Holder, Warren Hehre, Chris Cramer, Don Truhlar, Karl Freed, and Steve Dixon. The topics will cover a background of the current EHT, ZDO and NDDO parameterisations, for ground and excited states, for various basis sets, several solvation methods, and some future directions of all valence methods. It is anticipated that it will cover 1 1/2 days. I will post a more complete schedule later! See you there! Regards, -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From jsb2@camsci.com Tue Nov 15 22:26:56 1994 Received: from camsci.com for jsb2@camsci.com by www.ccl.net (8.6.9/930601.1506) id VAA27644; Tue, 15 Nov 1994 21:53:55 -0500 From: Date: Tue, 15 Nov 94 21:53:05 EST Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA08121; Tue, 15 Nov 94 21:53:05 EST Message-Id: <9411160253.AA08121@camsci.com> To: chemistry@ccl.net, rs0thp@rohmhaas.com Subject: Re: CCL:mol file conversions to XYZ? Cc: rdruker@rohmhaas.com >Is there any software free or commercial that converts mol file >format connection tables (from the NCI database) to approximate >XYZ coordinates? The boring answer is that CS Chem3D Pro will do this. I'm working on the more interesting answer. It should be possible to script Chem3D to convert a whole bunch of these structures automatically, using AppleScript. I am pretty sure this can be done, but I don't really have much time to spend on it at the moment. Does anyone feel like taking a crack at it? Using ChemFinder, it should even be able to retain the CAS IDs. (additional information about both programs is available at http://www.camsci.com) Jonathan Brecher Cambridge Scientific Computing, Inc. jsb@camsci.com