From owner-chemistry@ccl.net Tue Nov 21 03:51:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA16782; Tue, 21 Nov 1995 03:47:07 -0500 Received: from hearnvax.nic.surfnet.nl for J.Nilsson@farm.RUG.NL by bedrock.ccl.net (8.7.1/950822.1) id DAA06842; Tue, 21 Nov 1995 03:47:05 -0500 (EST) Received: from mailhost.rug.nl by HEARNVAX.nic.SURFnet.nl (PMDF V4.2-12 #3330) id <01HXWFQUPVHC008QF7@HEARNVAX.nic.SURFnet.nl>; Tue, 21 Nov 1995 09:49:14 +0100 (MET) Received: from dep.farm.rug.nl by mailhost.rug.nl with SMTP (PP); Tue, 21 Nov 1995 09:46:39 +0100 Received: from novell_farm1.farm.rug.nl by dep.farm.rug.nl (JAA05038); Tue, 21 Nov 1995 09:41:07 +0100 Received: from FARM1/MAIL by novell_farm1.farm.rug.nl (Mercury 1.20); 21 Nov 95 10:04:21 MET Received: from MAIL by FARM1 (Mercury 1.20); 21 Nov 95 10:04:01 MET Date: Tue, 21 Nov 1995 10:03:59 +0100 (CET) From: Jonas Nilsson Subject: electronic energy from AM1? To: chemistry@ccl.net Message-id: Organization: Pharmacy Dept Groningen University X-Envelope-to: chemistry@ccl.net X-Mailer: Pegasus Mail for Windows (v2.01) Content-transfer-encoding: 7BIT Priority: normal Hallo! I have a small question concerning the electronic energy parameter generated during a AM1 single point calculation. We have a dataset consisting of 30 compounds and we are trying to correlate physico-chemical parameters with the retention-time (k) on different HPLC-columns. We have generated around 30 parameters, AM1 outputs included. In order to see the influence on the retention time from different parameters we have performed a principal component analyses and a PLS regression model. The mode seems OK, with reasonable Qsq and good fitting. Our problem is that one of the more significant components is explained mainly by the Electronic energy. My question therefore is: How should this parameter be interpreted? How is this parameter calculated and what does it describe? Thanks, jonas e-mail: j.nilsson@farm.rug.nl From owner-chemistry@ccl.net Tue Nov 21 06:21:27 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA18803; Tue, 21 Nov 1995 06:16:04 -0500 Received: from mail.Germany.EU.net for jfk%biosym.uucp@Germany.EU.net by bedrock.ccl.net (8.7.1/950822.1) id GAA07333; Tue, 21 Nov 1995 06:15:50 -0500 (EST) Received: by mail.Germany.EU.net with UUCP (5.59:10/EUnetD-2.5.2.e) via EUnet id MAA21949; Tue, 21 Nov 1995 12:12:00 +0100 Received: by biosym (920330.SGI/920502.SGI.AUTO) id AA17465; Tue, 21 Nov 95 11:56:38 +0100 Date: Tue, 21 Nov 95 11:56:38 +0100 From: jfk%biosym.uucp@Germany.EU.net (Dr.J.F. Komorowski) Message-Id: <9511211056.AA17465@biosym> To: raaska@csc.fi, IMK832@UCLA.HDI.KFK.D400.DE, m.taylor@pra.org.uk, chemistry@ccl.net, jfh@biosym.com, DEBAYM59@IBMMAIL.COM, M.Wessling@ct.utwente.nl, pohlmann@igt.kfk.d400.de, cmeyer@physik.uni-osnarbrueck.de, brun0630@w418zrz.chem.tu-berlin.de Subject: I leave BIOSYM Dear Customers and Colleagues, as some of you might already know I will leave BIOSYM Technologies GmbH on December 31st '95. I'd like to express that it was great fun to interact with all of you. I will miss the valuable scientific cooperation we had during the last months. Also, I enjoyed the time we spent together at the most exciting locations of the world. On January 1 st I will take up a post in Siemens Nixdorf which will involve responsibilities in marketing and sales. I'll work in the IT-area with a strong focus on partnering projects with academic institutions and supercomputing centers in South-Germany. I leave "the science-playground" with a "laughing and a crying eye" (this is a german saying but I guess there are translations to any language). It'll be an exceptional opportunity for me on one hand. On the other hand I'm pretty sure that I'll suffer from the necessity of wearing suits and ties rather than jeans and BIOSYM T-shirts. I am already in hard negotiations with Simon Tomlinson to get one of his used ties (The red one with the nice stripes, pure silk as he says) but since he has much more experience in sales than I have I'm sure that I will make a bad deal. Since Siemens Nixdorf has offices all over the world I am convinced that sooner or later I will meet some of you sometimes somewhere on the globe again. Looking forward to seeing you Joachim PS: A f t e r the 31 st of December please send support requests to rcenter@biosym.com , they will then be assigned to an appropriate person in Europe or the US. PPS: I will have an e-mail account in Siemens Nixdorf, the address is yet not known. Please keep on sending any e-mail for me to jfk%biosym@germany.eu.net ; it will be forwarded and also a message with my new address in SNI will automaticly be returned. ____________________________________________________________________ Dr. Joachim F. Komorowski BIOSYM Technologies GmbH Tel.: ++ 49 89 42 93 22 Schatzbogen 54 FAX : 42 81 50 D-81829 Muenchen, Germany E-Mail: jfk%biosym@germany.eu.net ____________________________________________________________________ From owner-chemistry@ccl.net Tue Nov 21 07:21:24 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA19455; Tue, 21 Nov 1995 07:11:24 -0500 Received: from relay5.UU.NET for frisch@lorentzian.com by bedrock.ccl.net (8.7.1/950822.1) id HAA07519; Tue, 21 Nov 1995 07:11:22 -0500 (EST) Received: from uucp4.UU.NET by relay5.UU.NET with SMTP id QQzquq21179; Tue, 21 Nov 1995 07:11:22 -0500 (EST) Received: from m10.UUCP by uucp4.UU.NET with UUCP/RMAIL ; Tue, 21 Nov 1995 07:11:22 -0500 Received: from mjf by m10.lorentzian.com; Mon, 20 Nov 1995 22:12:51 -0500 Received: by mjf (AIX 4.1/UCB 5.64/4.03) id AA14874; Mon, 20 Nov 1995 22:12:50 -0500 From: frisch@lorentzian.com (Mike Frisch) Message-Id: <9511210312.AA14874@mjf> Subject: Clarification on Gaussian 94 NMR To: chemistry@ccl.net Date: Mon, 20 Nov 1995 22:12:50 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Content-Type: text The Gaussian manual is incorrect when it states that only pure DFT can be used to compute NMR shielding tensors; hybrid functionals also work fine. This is covered in the release notes. (The only coupling in the CPKS for the hybrid functions comes from the "exact" (HF) exchange term; this part is the same as for HF shielding tensors except for the scale factor. Of course, the right-hand sides of the linear equations are different in the two cases.) Mike Frisch frisch@lorentzian.com From 94970459@vax1.dcu.ie Tue Nov 21 08:21:27 1995 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.6.10/950822.1) id IAA20393; Tue, 21 Nov 1995 08:19:07 -0500 Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01HXVTUEP23K96VK5U@vax1.dcu.ie>; Mon, 20 Nov 1995 23:23:07 GMT Date: Mon, 20 Nov 1995 23:23:07 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Molecular Mechanics To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@www.ccl.net Message-id: <01HXVTUEQ4OI96VK5U@vax1.dcu.ie> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"hyperchem@hyper.com", IN%"support@hyper.com" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, I am a HyperChem user and I have two questions about molecular mechanics (MM): I recently asked the following question > While I know that the energies obtained in an MM calculation have > no absolute meaning, would the difference in energies of two > optimized conformations of the same complex have any meaning? If > so, what kind of energy are we talking about? What I wanted to know but did not specifically ask (typical of the way I ask questions!!!!!) is that if I have two different complexes where the ligand is the same but the ion is different what is the significance of the difference in energy resulting from an (MM) optimization? The reason that I ask is that I obtained the following energies from MM optimizations for complexes of the same ligand but with different ions: Energy/ (kcal / mol) Li+ -190.6 Na+ -171.2 K+ -150.8 We have found experimentally that the ligand is selective for sodium over magnesium; so I would have expected to have obtained a lower energy for the sodium complex. So *IF* MM optimization energies are not a reliable indicator of selectively what exactly is the significance of the above difference of 63 kcal / mol? The above optimizations were carried out by assigning the atom types to the metals published by Grootenhuis and Kollman, JACS., 1989, 111, 2152-2158. However I am not aware of the existence of atom types in the case of Group 2 metals and so I propose to use Noble Gas atoms as substitutes with charges of 2+ but I am not certain as to what atom types to use. Should I use the Noble Gas atom types that are part of the MM+ force field or should I leave the atom type as **. Regards, Paddy Paddy Kane E.mail: 94970459@vax1.dcu.ie School of Chemical Sciences Dublin City University Dublin Ireland From mn1@helix.nih.gov Tue Nov 21 10:51:28 1995 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.6.10/950822.1) id KAA22793; Tue, 21 Nov 1995 10:43:53 -0500 Received: (from mn1@localhost) by helix.nih.gov (8.6.12/8.6.12) id KAA14855; Tue, 21 Nov 1995 10:43:50 -0500 Date: Tue, 21 Nov 1995 10:43:50 -0500 From: "M. Nicklaus" Message-Id: <199511211543.KAA14855@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Need 1',6'-Methano Carbocyclic Thymidine coordinates Cc: mn1@helix.nih.gov Netters, Could someone please help us out and send me the coordinates (fdat, pdb, or xr format) of the X-ray structure of 1',6'-Methano Carbocyclic Thymidine (Altmann et al., Tet. Lett. 35(41), 7625-7628 (1994))? We have access to the CSD but don't have the newest version yet, which should contain this structure. Thanks in advance, Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 ------------------------------------------------------------------------ From owner-chemistry@ccl.net Tue Nov 21 11:21:29 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA23624; Tue, 21 Nov 1995 11:11:10 -0500 Received: from phem3 for U54632@UICVM.CC.UIC.EDU by bedrock.ccl.net (8.7.1/950822.1) id LAA09629; Tue, 21 Nov 1995 11:11:09 -0500 (EST) Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HXWIMCCDSG99DGH3@phem3.acs.ohio-state.edu>; Tue, 21 Nov 1995 11:11:06 EST Received: from UICVM (NJE origin U54632@UICVM) by UICVM.CC.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 3372; Tue, 21 Nov 1995 10:10:33 -0600 Date: Tue, 21 Nov 1995 10:06:06 -0600 (CST) From: U54632%UICVM.BITNET@phem3.acs.ohio-state.edu Subject: Conversion of Sybyl file format to PDB file format To: chemistry@ccl.net Message-id: <01HXWIMCCNFM99DGH3@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I'd like to know if there is a software, a free-bee, on the net that can convert a Sybyl (*.MO2) file to a PDB file. Any help would be highly appreciated. Thanks in advance -Chaya Email: U54632@uicvm.uic.edu From owner-chemistry@ccl.net Tue Nov 21 14:21:32 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA27970; Tue, 21 Nov 1995 14:19:47 -0500 Received: from camsci.com for jsb2@camsci.com by bedrock.ccl.net (8.7.1/950822.1) id OAA11548; Tue, 21 Nov 1995 14:19:43 -0500 (EST) From: Date: Tue, 21 Nov 95 14:19:31 EST Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA24682; Tue, 21 Nov 95 14:19:31 EST Message-Id: <9511211919.AA24682@camsci.com> To: U54632@UICVM.bitnet, chemistry@ccl.net Subject: Re: CCL:Conversion of Sybyl file format to PDB file format >I'd like to know if there is a software, a free-bee, on the net that can >convert a Sybyl (*.MO2) file to a PDB file. CS Chem3D Pro is not free, but it can do this conversion If simply viewing the models is enough, then CS Chem3D Net will do the trick, and it *is* freely available -- from http://www.camsoft.com among other places. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From A.T.Yagnik@exeter.ac.uk Tue Nov 21 14:51:30 1995 Received: from hermes for A.T.Yagnik@exeter.ac.uk by www.ccl.net (8.6.10/950822.1) id OAA28546; Tue, 21 Nov 1995 14:40:10 -0500 From: Received: from cen by hermes via ESMTP (TAA29569); Tue, 21 Nov 1995 19:39:40 GMT Message-Id: <12160.199511211939@cen> Subject: Re: CCL:Conversion of Sybyl file format to PDB file format To: CHEMISTRY@www.ccl.net Date: Tue, 21 Nov 1995 19:39:37 +0000 (GMT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1100 HI Chaya, > I'd like to know if there is a software, a free-bee, on the net that can > convert a Sybyl (*.MO2) file to a PDB file. You might want to try a program called Babel, by Pat Walters and Matt Stahl at The Dept. of Chemstry, University of Arizona. I think their Email is babel@mercury.aichem.arizona.edu Babel is capable of interconverting between lots of different formats. Hope this has helped. Regards, Tosh -- =============================================================================== Asutosh T Yagnik, Tel: (+44) 1392 263451 Protein Structure Group, Fax: (+44) 1392 263434 Department of Chemistry, Email: ATYagnik@exeter.ac.uk University of Exeter, * * WWW: http://www.exeter.ac.uk/ Stocker Road, Exeter. EX4 4QD. UK. > ~ATYagnik/ATYagnik \__/ {All opinions are my own!} "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi =============================================================================== From owner-chemistry@ccl.net Tue Nov 21 16:06:31 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA00495; Tue, 21 Nov 1995 15:59:18 -0500 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by bedrock.ccl.net (8.7.1/950822.1) id PAA12551; Tue, 21 Nov 1995 15:59:14 -0500 (EST) Received: from [128.109.178.113] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id PAA10800; Tue, 21 Nov 1995 15:59:11 -0500 for Date: Tue, 21 Nov 1995 15:59:11 -0500 Message-Id: <199511212059.PAA10800@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: gotwals@mcnc.org (Bob Gotwals) Subject: Carnegie Mellon Quantum Chem Archive... Does this resource still exist? If so, can someone provide me with an address? Thanks in advance.... From owner-chemistry@ccl.net Tue Nov 21 19:36:34 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA04007; Tue, 21 Nov 1995 19:22:06 -0500 Received: from phem3 for U54632@UICVM.CC.UIC.EDU by bedrock.ccl.net (8.7.1/950822.1) id TAA14228; Tue, 21 Nov 1995 19:22:05 -0500 (EST) Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HXWZQTJUSG99DHZT@phem3.acs.ohio-state.edu>; Tue, 21 Nov 1995 19:21:52 EST Received: from UICVM (NJE origin U54632@UICVM) by UICVM.CC.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 0609; Tue, 21 Nov 1995 18:21:22 -0600 Date: Tue, 21 Nov 1995 18:18:23 -0600 (CST) From: Chaya Duraiswami Subject: Summary of responses for the question on file format conversion To: chemistry@ccl.net Message-id: <01HXWZQTJUSI99DHZT@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I would like to thank everyone that responded with helpful suggestions to the question I had posted earlier, on the net. My inital posting on the net was: ______________________________________________________________________ >Subject: Conversion of Sybyl file format to PDB file format > >I'd like to know if there is a software, a free-bee, on the net that can >convert a Sybyl (*.MO2) file to a PDB file. > >Any help would be highly appreciated. > >Thanks in advance >-Chaya ______________________________________________________________________ Most of the suggestions were that I should try "Babel". And indeed, "Babel" does the trick nicely! To access babel: 1. Email babel@mercury.aichem.arizona.edu 2. ftp://joplin.biosci.arizona.edu/pub/Babel 3. check out CCL archives 4. http://mercury.aichem.arizona.edu/babel.html 5. ftp tutor.oc.chemie.th-darmstadt.de The other suggestions were: 1. try Hyperchem - a commercial software 2. CS Chem3D Pro, which is not free. But, if simply viewing the models is enough, then CS Chem3D Net will do the trick, and it *is* freely available -- from http://www.camsoft.com Thank you once again! Sincerely, Chaya Duraiswami From CTARG@Levels.UniSA.Edu.Au Tue Nov 21 20:36:35 1995 Received: from bROLga.Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by www.ccl.net (8.6.10/950822.1) id UAA04795; Tue, 21 Nov 1995 20:29:26 -0500 From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HXXYL1818G9AMGIU@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 22 Nov 1995 11:59:13 +0930 Date: Wed, 22 Nov 1995 11:59:13 +0930 Subject: quantum mechanics summer schools? To: chemistry@www.ccl.net Message-id: <01HXXYL19DGY9AMGIU@Levels.UniSA.Edu.Au> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, For the last couple (?) of years there has been a quantum mechanics summer school held in Italy. Could somebody tell me whether there is going to be one in 1996 and where and when it is going to be held? Thanks Andrea.