From chemistry-request@server.ccl.net Thu Dec 17 03:32:46 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA03373 for ; Thu, 17 Dec 1998 03:32:46 -0500 Received: from panter.icpf.cas.cz (www.ataxb.cz [194.108.106.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA29701 Thu, 17 Dec 1998 03:29:57 -0500 (EST) Received: by panter.icpf.cas.cz with Internet Mail Service (5.0.1460.8) id ; Thu, 17 Dec 1998 09:27:59 +0100 Message-ID: From: Ponec Robert EXCHANGE To: CCL Subject: question Date: Thu, 17 Dec 1998 09:27:58 +0100 X-MS-TNEF-Correlator: MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BE2997.27667D42" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------ =_NextPart_000_01BE2997.27667D42 Content-Type: text/plain Dear CCL`ers I have a question concerning the internet address of web pages of PC Gamess. I have used until recently one but this seems to have been changed and I can no more uyse it. Does anybody knows the new localtion of these pages? Many thanks, Robert Ponec Institute of Chemical Process Fundamentals Czech Academy of Sciences Prague 6, Suchdol 2 165 02 Czech Republic fax: 420 2 20920661 tel:420 2 20390271 email: rponec@icpf.cas.cz ------ =_NextPart_000_01BE2997.27667D42 Content-Type: application/ms-tnef Content-Transfer-Encoding: base64 eJ8+IjwIAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA4gQAAAAAAADmAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQWAAwAOAAAAzgcMABEACQAbADoABABUAQEggAMADgAAAM4HDAAR AAkAGwA7AAQAVQEBCYABACEAAABDMjQ2NDRFNDFEOTNEMjExQTVFNzAwNjA4Q0U4RUNCRgA5BwEE gAEACgAAAHF1ZXN0aW9uIACYAwENgAQAAgAAAAIAAgABA5AGAEwGAAApAAAACwACAAEAAABAADkA 4Gs0J5cpvgEeAHAAAQAAAAoAAABxdWVzdGlvbiAAAAACAXEAAQAAABYAAAABvimXyCnkREbEkx0R 0qXnAGCM6Oy/AAAeADFAAQAAAAcAAABSUE9ORUMAAAMAGkAAAAAAHgAwQAEAAAAHAAAAUlBPTkVD AAADABlAAAAAAAIBCRABAAAANgIAADICAADUAgAATFpGdTkCbFADAAoAcmNwZzEyNdMBQwE3MzYB 6CACpwIABGNoCsBzZXQwIPhUYWgDcQKDAFAD1BCXqDIzOAAAKgLhYQeAjiAHEwKABxMgQ0UCgHJ9 CoF1YwBQCwMLYG4RDhAwMzMLpiBEZeEKwUNDTGAEkBJgCrFTCoQKgEkgEMB2E7BhRCBxClBzdGkC ICAZBaBuYwSRC4BnIHR2aBOwC4B0BJERABigZAZkCXAEEW9mIHdlNGIgCrBnB5EbYVBDTCBHE5EE EC4gGEV1/RDwZB1wAjADEQlwGZACMIxseRtQGqAgYnUFQEsaEAQAIBDwZW0EIHT6bxhUYgnhGVAQ wBXQHaHXAHAdsBhAYwORbiAABGBbCXAdcHkQ8BpAdBzwRFZvB5EAcHkG4GQeoGv9IeB3H9EaIRqg B+AJACGgvmwZExthGhEigRvTPxeKjk0jQRoBAHBrcywVpTwyORHSF5kK9AuzMTf/B/EgcAAgHFAe wQDgF/QAgF0ZEHQfEBOwG2FDGiBtuw3gFHFQA2AZkAQRRh3QnmQTkQIwB0AXdUN6BZBuaBPAIaAB AG0eoRtwU35jCJAZgRd1LJAb4ApQIEw2LAYAFSBoZAbwIMIyF4QxNjUgKBAUkOEuQ1JlcHUCYA3g F4TAZmF4OiA0FpEyAGUB0DkB0DY2KGUacGzSOjO2MzkoEDcoZR+wVwtwNRAeIHAqkkAN4WbmLiGg HOBjeih/EdQMAQsXkxThADowAAALAACACCAGAAAAAADAAAAAAAAARgAAAAADhQAAAAAAAAMAAoAI IAYAAAAAAMAAAAAAAABGAAAAABCFAAAAAAAAAwAFgAggBgAAAAAAwAAAAAAAAEYAAAAAUoUAALcN AAAeACWACCAGAAAAAADAAAAAAAAARgAAAABUhQAAAQAAAAQAAAA4LjAAAwAmgAggBgAAAAAAwAAA AAAAAEYAAAAAAYUAAAAAAAALAC+ACCAGAAAAAADAAAAAAAAARgAAAAAOhQAAAAAAAAMAMIAIIAYA AAAAAMAAAAAAAABGAAAAABGFAAAAAAAAAwAygAggBgAAAAAAwAAAAAAAAEYAAAAAGIUAAAAAAAAe AEGACCAGAAAAAADAAAAAAAAARgAAAAA2hQAAAQAAAAEAAAAAAAAAHgBCgAggBgAAAAAAwAAAAAAA AEYAAAAAN4UAAAEAAAABAAAAAAAAAB4AQ4AIIAYAAAAAAMAAAAAAAABGAAAAADiFAAABAAAAAQAA AAAAAAADAPE/CQQAAAMA/T/iBAAAAwAmAAAAAAADADYAAAAAAAMAgBD/////AgFHAAEAAAAsAAAA Yz1DWjthPSA7cD1BVkNSO2w9UEFOVEVSLTk4MTIxNzA4Mjc1OFotMTE2MgAeADhAAQAAAAcAAABS UE9ORUMAAB4AOUABAAAABwAAAFJQT05FQwAAQAAHMOBrNCeXKb4BQAAIMEJ9ZieXKb4BHgA9AAEA AAABAAAAAAAAAB4AHQ4BAAAACgAAAHF1ZXN0aW9uIAAAAB4ANRABAAAAPAAAADxENjYxNDM2RTU1 MjVEMTExOEEzRTAwQTBDOTE0MTNERTJGNjY1MEBwYW50ZXIuaWNwZi5jYXMuY3o+AAsAKQAAAAAA CwAjAAAAAAADAAYQWYpvwQMABxBnAQAAAwAQEAAAAAADABEQAAAAAB4ACBABAAAAZQAAAERFQVJD Q0xFUlNJSEFWRUFRVUVTVElPTkNPTkNFUk5JTkdUSEVJTlRFUk5FVEFERFJFU1NPRldFQlBBR0VT T0ZQQ0dBTUVTU0lIQVZFVVNFRFVOVElMUkVDRU5UTFlPTkVCVVQAAAAAAgF/AAEAAAA8AAAAPEQ2 NjE0MzZFNTUyNUQxMTE4QTNFMDBBMEM5MTQxM0RFMkY2NjUwQHBhbnRlci5pY3BmLmNhcy5jej4A +kU= ------ =_NextPart_000_01BE2997.27667D42-- From chemistry-request@server.ccl.net Thu Dec 17 06:08:05 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03593 for ; Thu, 17 Dec 1998 06:08:04 -0500 Received: from athe.wustl.edu (athe.wustl.edu [128.252.122.173]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA00245 Thu, 17 Dec 1998 06:05:13 -0500 (EST) Received: (from toni@localhost) by athe.wustl.edu (8.9.1/8.9.1) id FAA26649; Thu, 17 Dec 1998 05:04:13 -0600 (CST) Date: Thu, 17 Dec 1998 05:04:13 -0600 (CST) From: Toni Kazic Message-Id: <199812171104.FAA26649@athe.wustl.edu> To: Rponec@icpf.cas.cz CC: chemistry@www.ccl.net In-reply-to: (message from Ponec Robert EXCHANGE on Thu, 17 Dec 1998 09:27:58 +0100) Subject: Re: CCL:question http://www.msg.ameslab.gov/GAMESS/GAMESS.html will get you to the main page with pointers from there. Toni From chemistry-request@server.ccl.net Thu Dec 17 08:04:58 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03611 for ; Thu, 17 Dec 1998 08:04:57 -0500 Received: from panter.icpf.cas.cz (panter.icpf.cas.cz [147.231.136.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA00658 Thu, 17 Dec 1998 08:02:06 -0500 (EST) Received: by panter.icpf.cas.cz with Internet Mail Service (5.0.1460.8) id ; Thu, 17 Dec 1998 14:00:30 +0100 Message-ID: From: Ponec Robert EXCHANGE To: CCL Subject: reply to question Date: Thu, 17 Dec 1998 14:00:30 +0100 X-MS-TNEF-Correlator: MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BE29BD.39A03AF4" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------ =_NextPart_000_01BE29BD.39A03AF4 Content-Type: text/plain Dear CCl`ers thanks to all who replied to my quation concerning the address of the PC gamess web pages. Robert Ponec Institute of Chemical Process Fundamentals Czech Academy of Sciences Prague 6, Suchdol 2 165 02 Czech Republic fax: 420 2 20920661 tel:420 2 20390271 email: rponec@icpf.cas.cz ------ =_NextPart_000_01BE29BD.39A03AF4 Content-Type: application/ms-tnef Content-Transfer-Encoding: base64 eJ8+Ih8NAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA4gQAAAAAAADmAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQWAAwAOAAAAzgcMABEADgAAAB4ABAAiAQEggAMADgAAAM4HDAAR AA4AAAAeAAQAIgEBCYABACEAAABGQ0JEOEZEQjhGOTVEMjExQTVFNzAwNjA4Q0U4RUNCRgCXBwEE gAEAEgAAAHJlcGx5IHRvIHF1ZXN0aW9uAMcGAQ2ABAACAAAAAgACAAEDkAYA2AUAACkAAAALAAIA AQAAAEAAOQCQC3o5vSm+AR4AcAABAAAAEgAAAHJlcGx5IHRvIHF1ZXN0aW9uAAAAAgFxAAEAAAAW AAAAAb4pvdpv24+9/pWPEdKl5wBgjOjsvwAAHgAxQAEAAAAHAAAAUlBPTkVDAAADABpAAAAAAB4A MEABAAAABwAAAFJQT05FQwAAAwAZQAAAAAACAQkQAQAAALQBAACwAQAAOAIAAExaRnV5d9gAAwAK AHJjcGcxMjXTAUMBNzM2AeggAqcCAARjaArAc2V0MCD4VGFoA3ECgwBQA9QQl6gyMzgAACoC4WEH gI4gBxMCgAcTIENFAoByfQqBdWMAUAsDC2BuEQ4QMDMzC6YgRGXhCsFDQ2xgBJASYAqxSwqECoB0 EMBuawQgdKxvIAdAAyB3EWAgCXALC1AIkGQYom15IHFQdWF0aQIgIAWgblZjBJELgGcYoGgTsGFM ZGQJcAQRb2YbY1AYQyBnE5EEEXdlYmogCrBnB5AuAzAVtDKeORHSF5kK9AuzMTcH8XZiBJAFQFAC IAWQF4RJYwCAGnB0dXQTsBwxQ+0bgG0N4BRxUANgGvAEEfBGdW5kE5ECMAdAF3X0Q3oFkGgTwCKQ AQAaEfkcMVNjCJAa4Rd1ItAdkDEKUCA2LAYAFSBoZAkG8CAyF4QxNjUg1x5QFJAkg1IZcHUCYA3g gReEZmF4OiA0FpHLKEAB0DkB0DY2HqUh4KRsOin2MzkeUDcepa8iYAtwK1AZUHAg0kAN4cxmLiKQ HcBjeh6/EdQXDAEXkxThADBwCwAAgAggBgAAAAAAwAAAAAAAAEYAAAAAA4UAAAAAAAADAAKACCAG AAAAAADAAAAAAAAARgAAAAAQhQAAAAAAAAMABYAIIAYAAAAAAMAAAAAAAABGAAAAAFKFAAC3DQAA HgAlgAggBgAAAAAAwAAAAAAAAEYAAAAAVIUAAAEAAAAEAAAAOC4wAAMAJoAIIAYAAAAAAMAAAAAA AABGAAAAAAGFAAAAAAAACwAvgAggBgAAAAAAwAAAAAAAAEYAAAAADoUAAAAAAAADADCACCAGAAAA AADAAAAAAAAARgAAAAARhQAAAAAAAAMAMoAIIAYAAAAAAMAAAAAAAABGAAAAABiFAAAAAAAAHgBB gAggBgAAAAAAwAAAAAAAAEYAAAAANoUAAAEAAAABAAAAAAAAAB4AQoAIIAYAAAAAAMAAAAAAAABG AAAAADeFAAABAAAAAQAAAAAAAAAeAEOACCAGAAAAAADAAAAAAAAARgAAAAA4hQAAAQAAAAEAAAAA AAAAAwDxPwkEAAADAP0/4gQAAAMAJgAAAAAAAwA2AAAAAAADAIAQ/////wIBRwABAAAAKwAAAGM9 Q1o7YT0gO3A9QVZDUjtsPVBBTlRFUi05ODEyMTcxMzAwMzBaLTEzNwAAHgA4QAEAAAAHAAAAUlBP TkVDAAAeADlAAQAAAAcAAABSUE9ORUMAAEAABzD6snc5vSm+AUAACDD0OqA5vSm+AR4APQABAAAA AQAAAAAAAAAeAB0OAQAAABIAAAByZXBseSB0byBxdWVzdGlvbgAAAB4ANRABAAAAPAAAADxENjYx NDM2RTU1MjVEMTExOEEzRTAwQTBDOTE0MTNERTJGOTA4OUBwYW50ZXIuaWNwZi5jYXMuY3o+AAsA KQAAAAAACwAjAAAAAAADAAYQfTasBgMABxDyAAAAAwAQEAAAAAADABEQAAAAAB4ACBABAAAAZQAA AERFQVJDQ0xFUlNUSEFOS1NUT0FMTFdIT1JFUExJRURUT01ZUVVBVElPTkNPTkNFUk5JTkdUSEVB RERSRVNTT0ZUSEVQQ0dBTUVTU1dFQlBBR0VTUk9CRVJUUE9ORUNJTlNUSVQAAAAAAgF/AAEAAAA8 AAAAPEQ2NjE0MzZFNTUyNUQxMTE4QTNFMDBBMEM5MTQxM0RFMkY5MDg5QHBhbnRlci5pY3BmLmNh cy5jej4Atio= ------ =_NextPart_000_01BE29BD.39A03AF4-- From chemistry-request@server.ccl.net Thu Dec 17 09:08:13 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03626 for ; Thu, 17 Dec 1998 09:08:12 -0500 Received: from techunix.technion.ac.il (root@techunix.technion.ac.il [132.68.1.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA01134 Thu, 17 Dec 1998 09:05:12 -0500 (EST) Received: from tx.technion.ac.il (cedl09.technion.ac.il [132.68.80.95]) by techunix.technion.ac.il (8.9.1/8.8.5) with ESMTP id QAA09590; Thu, 17 Dec 1998 16:04:52 +0200 (IST) Message-ID: <36791AF7.CFB1FE6@tx.technion.ac.il> Date: Thu, 17 Dec 1998 16:53:43 +0200 From: Irena Efremenko Organization: Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000 X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Computational Chemistry List CC: Faya Dubnikova Subject: geometry optimization for f-elements Content-Type: multipart/mixed; boundary="------------1FD749855CD7EF99DC198B0B" This is a multi-part message in MIME format. --------------1FD749855CD7EF99DC198B0B Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, A friend of mine is interested to perform geometry optimizations for small molecules on surfaces of uranium oxide. The level of calculations may be low (EH or other semiempirical methods) . Any suggestions will be approciated. Thanks in advance, Irena Efremenko --------------1FD749855CD7EF99DC198B0B Content-Type: text/x-vcard; charset=koi8-r; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Irena Efremenko Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Irena Efremenko n: Efremenko;Irena org: Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel email;internet: chrirena@tx.technion.ac.il title: Dr. tel;work: (972) 4 8293561 tel;fax: (972) 4 8230479 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------1FD749855CD7EF99DC198B0B-- From chemistry-request@server.ccl.net Thu Dec 17 10:04:33 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03730 for ; Thu, 17 Dec 1998 10:04:33 -0500 Received: from gatekeeper.tripos.com (gatekeeper.tripos.com [38.154.18.254]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA01737 Thu, 17 Dec 1998 10:01:39 -0500 (EST) Received: (from uucp@localhost) by tripos.com (SMI-8.6) id JAA19220 for <@firewall.tripos.com:chemistry@www.ccl.net>; Thu, 17 Dec 1998 09:00:13 -0600 Received: from elara.tripos.com(192.160.145.60) by gatekeeper.tripos.com via smap (4.1) id xma019195; Thu, 17 Dec 98 08:59:45 -0600 Received: from tripos.com (thebe [192.160.145.47]) by tripos.com (980919.SGI.STAND) via ESMTP id IAA86379 for ; Thu, 17 Dec 1998 08:59:45 -0600 (CST) Sender: dlarson@elara.tripos.com Message-ID: <36791C62.320414CE@tripos.com> Date: Thu, 17 Dec 1998 08:59:46 -0600 From: David Larson Reply-To: bclark@tripos.com Organization: Tripos, Inc. X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re:Enhancing CoMFA:free program release References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Arthur Wang recently posted a message to CCL announcing avaiability of SPL programs which "improve" CoMFA analyses by exhaustively searching the possible orientations and placements of molecules on the lattice and using that which gives the highest q^2. Users should be aware that when this is done, that highest q^2 ceases to be a valid test statistic for the significance of the model and no longer accurately reflects the expected external predictivity, just as is the case for variable selection methods in general( see U Norinder J. Chemonetrics 1996, 10, 95-105 and recent reports by other groups). This is because compounds are no longer completely "left out" of the analysis - each contributes to identifying the highest q^2. A lattice shift represents a random perturbation of the CoMFA descriptors. Though neither the highest nor the lowest q^2 value are of interest in and of themselves, the AOS and APS programs may nonetheless be useful for determining the distribution of values and hence how robust a particular model (the scheme used to align each molecule with the others) is. When this is done, however, the appropriate test statistic is the median or mode q^2 or, better, the mean cross-validated standard error and the q^2 calculated therefrom. Lattice placements which give q^2 values at either extreme - high or low - are misleading and therefore undesirable. It turns out, however, that good representative lattice orientations can reliably be obtained simply by applying ORIENT BEST to a prototypical molecular (usually the most extended of the more active compounds) and aligning other molecules in the training set on that prototype (RD Clark, M Cline & TW Heritage (1998) Making 3D QQSAR Both Simple and Robust, 215 ACS Natl Meeting, Abstract COMP 057). In fact, this is now the default option in the DATABASE ALIGNMENT dialog in SYBYL QSAR. Bob Clark Tripos Inc. 1699 S. Hanley Road St. Louis MO 63144 bclark@tripos.com