From tomas.oberg@bergstrom-oberg.se Mon Oct 20 04:31:52 1997 Received: from mailb.telia.com for tomas.oberg@bergstrom-oberg.se by www.ccl.net (8.8.3/950822.1) id EAA13491; Mon, 20 Oct 1997 04:29:08 -0400 (EDT) Received: from d1o23.telia.com (root@d1o23.telia.com [195.198.246.241]) by mailb.telia.com (8.8.5/8.8.5) with ESMTP id KAA14704 for ; Mon, 20 Oct 1997 10:28:51 +0200 (MET DST) Received: from t6o23p8.telia.com (t3o23p36.telia.com [195.198.246.156]) by d1o23.telia.com (8.8.5/8.8.5) with SMTP id KAA08099 for ; Mon, 20 Oct 1997 10:28:35 +0200 (MET DST) Received: by t6o23p8.telia.com with Microsoft Mail id <01BCDD43.137AE620@t6o23p8.telia.com>; Mon, 20 Oct 1997 10:29:41 +0200 Message-ID: <01BCDD43.137AE620@t6o23p8.telia.com> From: "Tomas Oberg, Bergstrom & Oberg" To: "'chemistry@www.ccl.net'" Subject: Experimental optimization newsletter Date: Mon, 20 Oct 1997 10:22:26 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable The MultiSimplex electronic newsletter will be published every second or = third month (4-6 issues/year). It is delivered free to users, and all = others that have shown interest in the MultiSimplex software for = experimental optimization. The first issue is due this week. Contents 1. Editorial 2. New approaches to experimental optimization and empirical = model-building. 3. A successful application story - MultiSimplex at work in the = laboratory. 4. New patches. Free upgrade for registered users. New subscriptions are easy to add, just send us an email with the = request. Best regards, Tomas Oberg Multisimplex KB info@multisimplex.com www.multisimplex.com From pang@iris.chem.cuhk.edu.hk Sat Oct 18 02:31:27 1997 Received: from iris.chem.cuhk.edu.hk for pang@iris.chem.cuhk.edu.hk by www.ccl.net (8.8.3/950822.1) id BAA04213; Sat, 18 Oct 1997 01:56:15 -0400 (EDT) Received: by iris.chem.cuhk.edu.hk (940816.SGI.8.6.9/940406.SGI.AUTO) id NAA07622; Sat, 18 Oct 1997 13:57:07 +0800 Date: Sat, 18 Oct 1997 13:56:55 +0800 (HKT) From: Pang Siu Kwong To: chemistry@www.ccl.net Subject: free energy of solvation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII How are you? I am a beginner of computational chemistry. Is there any software or method to calculate the free energy of solvation of molecules. The parameters for energy of solvation includes dielectric constant of solvent, dipole-dipople interaction, van der Waals interaction and hydrogen bonding. Patrick Pang From ccl@www.ccl.net Mon Oct 20 00:31:48 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id AAA12465; Mon, 20 Oct 1997 00:29:08 -0400 (EDT) Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by bedrock.ccl.net (8.8.6/950822.1) id AAA25456; Mon, 20 Oct 1997 00:29:07 -0400 (EDT) From: Received: from localhost by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA20854; Mon, 20 Oct 1997 00:29:00 -0400 Date: Mon, 20 Oct 1997 00:29:00 -0400 (EDT) To: CCLink Subject: PCM calculations.. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, folks. Got a few questions concerning PCM for solvation effect, I'd appreciate any comments from the experts ouut there. 1. What would be a reasonable value for the # of points per atomic sphere? From one paper by Frisch et al., a value of 2000 is recommanded, I wonder if this is the case in general? 2. In a recent CPL paper by Tomasi et al., a new implementation of PCM, the so-called PCM/DIR has been reported. ANy one has any experience with it? or at least how to get it? 3. Is there any new development in the gradient calculations with PCM recently? Or, any other methods has analytical gradients? (besides Truhlar's g-Born and Troung's GCOSMO) 4. In several papers by Tomasi et al.,the SCIPCM of Frisch et al. was shown to be not as accurate for charged solute as for neutral ones, I wonder if any one has similar experience on this issue? 5. Finally, I'd appreciate any comments on solvation effect calculations of highly charged systems. Thanks! I'll summerize. ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From istvan@bioorg.ee.cua.edu Mon Oct 20 10:35:22 1997 Received: from pluto.ee.cua.edu for istvan@bioorg.ee.cua.edu by www.ccl.net (8.8.3/950822.1) id KAA15482; Mon, 20 Oct 1997 10:25:27 -0400 (EDT) Received: from bioorg.ee.cua.edu (bioorg.ee.cua.edu [136.242.140.81]) by pluto.ee.cua.edu (8.8.5/8.8.5) with SMTP id KAA08549 for <@pluto.ee.cua.edu:chemistry@www.ccl.net>; Mon, 20 Oct 1997 10:30:10 -0400 Received: by bioorg.ee.cua.edu (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA18232; Mon, 20 Oct 1997 10:35:29 -0400 From: "Istvan Enyedy" Message-Id: <9710201035.ZM18230@bioorg.ee.cua.edu> Date: Mon, 20 Oct 1997 10:35:27 -0400 Reply-to: istvan@bioorg.ee.cua.edu X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: proton transfer Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, I would like to ask if any of you has information about theoretical calculations for proton transfer in biological systems. I am interested to know the time scale of these proccesses and the geometry for proton transfer to an acceptor. I will summerize the answers. Thank you, Istvan -- ************************************************* Istvan Enyedy The Catholic University of America Chemistry Department/ Maloney Hall Washington DC 20064 email istvan@bioorg.ee.cua.edu phone 202-319-5707 or 5349 fax 202-319-5381 ************************************************** From jlthomas@mail.smu.edu Mon Oct 20 10:40:50 1997 Received: from post.cis.smu.edu for jlthomas@mail.smu.edu by www.ccl.net (8.8.3/950822.1) id KAA15439; Mon, 20 Oct 1997 10:13:32 -0400 (EDT) Received: by post.cis.smu.edu (Smail-3.2.0.96 1997-Jun-2 #26) id ; Mon, 20 Oct 1997 09:08:10 -0500 (CDT) Message-Id: In-Reply-To: <344385B4.59A957B5@guomai.sh.cn> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Oct 1997 09:09:04 -0600 To: Yubo Fan , Computational Chemistry List From: Julie Thomas Subject: Re: CCL:Need Job Samples of G94 with opt=QST2 or QST3 At 10:46 PM +0800 10/14/97, Yubo Fan wrote: >Hi, Netters, > >I tried some new methods of Gaussian 94 for optimization of Transition >States. I have some questions. When I use opt=QST3 option, can I use >cartesian coordination for the three molecular specifications. >If I can, could you please give some input file examples? > >Thank you very much > >Y. Fan Yubo, Here's an input example. Note that things work a lot more smoothly if the atoms are numbered in the same order in all three molecules. #p B3LYP/6-31g** pop=reg opt=qst3 scfcyc=100 guess=check H2C2B4H4 DFT closo Geometry 0 1 B 0.000000 1.218650 0.000000 B -0.020210 -1.218485 0.000000 C 0.729137 -0.006044 0.770928 C 0.729137 -0.006044 -0.770928 B -0.896179 0.007433 0.854660 B -0.896179 0.007433 -0.854660 H 0.213319 2.377593 0.000000 H 0.173781 -2.380816 0.000000 H 1.585949 -0.013113 1.428443 H 1.585949 -0.013113 -1.428443 H -1.622902 0.013410 1.784487 H -1.622902 0.013410 -1.784487 H2C2B4H4 DFT nido-apart Geometry -2 1 B 1.329358 0.000000 -0.312299 C 0.385232 1.221441 -0.235460 C 0.385232 -1.221441 -0.235460 B -1.140423 0.831213 -0.244145 B -1.140423 -0.831213 -0.244145 B -0.011608 0.000000 0.895023 H 0.158569 0.000000 2.100376 H 2.539991 0.000000 -0.083097 H 0.752053 2.209136 0.096806 H 0.752053 -2.209136 0.096806 H -2.004989 1.655963 0.071227 H -2.004989 -1.655963 0.071227 H2C2B4H4 DFT closo-nido guess Geometry -2 1 B -1.116552 -0.712118 0.316142 B 1.319388 0.415633 -0.438336 B 0.517915 -0.625567 0.906472 B 0.201176 1.345190 0.271473 C 0.374586 -0.844057 -0.642670 C -1.186995 0.654233 -0.254030 H 1.105716 -1.328091 1.709686 H 0.146800 2.334702 1.014366 H -1.910572 -1.654185 0.179768 H 2.545587 0.303318 -0.576434 H 0.316151 -1.741584 -1.274014 H -1.938866 1.109094 -0.951926 ! From mnolan@nmrc.ucc.ie Mon Oct 20 11:31:54 1997 Received: from bastion.nmrc.ucc.ie for mnolan@nmrc.ucc.ie by www.ccl.net (8.8.3/950822.1) id LAA15802; Mon, 20 Oct 1997 11:03:41 -0400 (EDT) Received: by nmrc.ucc.ie (8.6.12/8.6.6) with ESMTP id OAA01124 for ; Mon, 20 Oct 1997 14:02:08 +0100 From: Michael Nolan Message-Id: <199710201129.LAA08795@laredo.nmrc.ucc.ie> Subject: DFT software To: chemistry@www.ccl.net Date: Mon, 20 Oct 1997 11:29:20 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hello o great CCLers, My supervisor has asked me to communicate the following to you: Are there any downloadable (preferably free) programs for running DFT calculations on Windows95 and/or a HP machine? We already have Turbomole, but are running our DFT calculations as direct calculations. All answers gratefully accepted Michael ************************************************************************************** Michael Nolan Computational Chemist Materials Group National Microelectronics Research Centre Lee Maltings Prospect Row Cork IRELAND mnolan@nmrc.ucc.ie ************************************************************************************** From bear@ellington.Pharmacy.arizona.edu Mon Oct 20 14:31:57 1997 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id OAA17191; Mon, 20 Oct 1997 14:00:01 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id LAA20564 for chemistry@www.ccl.net; Mon, 20 Oct 1997 11:00:01 -0700 (MST) Date: Mon, 20 Oct 1997 11:00:01 -0700 (MST) From: Soaring Bear Message-Id: <199710201800.LAA20564@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: CCL:calculate bond order of conjugated pi system >2. Automatically identify conjugated pi-system. CCL would be an appropriate forum to discuss better ways of doing this, since even the premium software programs make mistakes in assignments due to variability in pdb structures. SOARING BEAR bear@pharmacy.arizona.edu O-topoisomerase Computational Medicinal Chemistry 5'*: :*.* Cancer Biochemistry & Drug Design |'*. .*'| | Protein & DNA Structural Biology | | *.,* | | | Pharmacognosy & Natural Dentistry 3'*.DNA helix| * http://ellington.pharm.arizona.edu/~bear '***' '**' From g-recht@chem.nwu.edu Mon Oct 20 17:31:59 1997 Received: from mercury.chem.nwu.edu for g-recht@chem.nwu.edu by www.ccl.net (8.8.3/950822.1) id RAA18744; Mon, 20 Oct 1997 17:15:59 -0400 (EDT) Received: (from g-recht@localhost) by mercury.chem.nwu.edu (8.8.5/8.8.5) id QAA07517 for chemistry@www.ccl.net; Mon, 20 Oct 1997 16:15:16 -0500 (CDT) From: Gregory Rechtsteiner Message-Id: <199710202115.QAA07517@mercury.chem.nwu.edu> Subject: Solvent Accessible Surface Area To: chemistry@www.ccl.net Date: Mon, 20 Oct 1997 16:15:16 -0500 (CDT) X-Mailer: ELM [version 2.5 PL0a3] Content-Type: text Hello: I know that the topic of solvent accessible surface areas of proteins has been discussed previously on this list. I am interested in obtaining a program (freeware or shareware or at a minimal cost), that can compute the solvent accessible surface areas of simple proteins, such as cytochrome c, myoglobin, etc. The program can be compiled for a DOS/Windows or Linus machine, or it can be Fortran or C code. Please let me know what programs are available; I wil summarize for those interested. Thank you, Greg -- Greg Rechtsteiner Department of Chemistry Northwestern University Evanston, IL 60208 g-recht@chem.nwu.edu