From chemistry-request@server.ccl.net Fri Jul 13 11:04:03 2001 Received: from smtp1.post.cz ([195.250.146.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6DF42501501 for ; Fri, 13 Jul 2001 11:04:02 -0400 Received: (from root@localhost) by smtp1.post.cz (8.11.2/8.11.2/Debian 8.11.2-1) id f6DF40P22870; Fri, 13 Jul 2001 17:04:00 +0200 From: sasha1@post.cz X-Priority: 1 MIME-Version: 1.0 Message-Id: <3B4F0DE0.000002.22854@smtp1> Date: Fri, 13 Jul 2001 17:03:37 +0200 (CEST) Content-Type: Text/Plain Content-Transfer-Encoding: 7bit To: chemistry@ccl.net Subject: Non-adiabatic molecular Hamiltonian - a not yet finished study ..... Some interesting details on ongoing studies of the adiabatic correction to the energy of molecular systems are given here: http://www.pandora.cz/mail.php3?no=755145 http://www.pandora.cz/mail.php3?no=755146 From chemistry-request@server.ccl.net Thu Jul 12 21:58:34 2001 Received: from web14309.mail.yahoo.com ([216.136.224.59]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6D1wY510338 for ; Thu, 12 Jul 2001 21:58:34 -0400 Message-ID: <20010713015833.80213.qmail@web14309.mail.yahoo.com> Received: from [161.142.10.11] by web14309.mail.yahoo.com via HTTP; Thu, 12 Jul 2001 18:58:33 PDT Date: Thu, 12 Jul 2001 18:58:33 -0700 (PDT) From: rabia rabia Subject: free energy and mic To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi friends! i have calculated the estimated free energies of binding, inhibition constants of different ligands by docking them into the enzyme with the help of program AUTODOCK. for some ligands i have the experimental MIC values. i want to correlate my results with these experimental MIC values. any suggestion of how i can get the theoretical mic values from free energy or inhibition constants. another ? the program autodock3 gives inhibition constant values, any suggestion of how i can rank my ligands with respect to the inhibition constant...or how i can analyze it.... Thanx in advance for suggestions. rabia. UNIVERSITY. __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Thu Jul 12 15:53:36 2001 Received: from c001.snv.cp.net ([209.228.32.132]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6CJrZ506892 for ; Thu, 12 Jul 2001 15:53:35 -0400 Received: (cpmta 5948 invoked from network); 12 Jul 2001 12:53:30 -0700 Date: 12 Jul 2001 12:53:30 -0700 Message-ID: <20010712195330.5947.cpmta@c001.snv.cp.net> X-Sent: 12 Jul 2001 19:53:30 GMT Received: from [199.98.21.13] by mail.roberttopper.com with HTTP; 12 Jul 2001 12:53:30 PDT Content-Type: text/plain Content-Disposition: inline Mime-Version: 1.0 To: CHEMISTRY@ccl.net From: Robert Topper Cc: roberttopper@roberttopper.com X-Mailer: Web Mail 3.9.3.5 Subject: Summary of SPARTAN 5.0 vs 5.1: coordinate driving X-Sent-From: roberttopper@roberttopper.com Summary of SPARTAN 5.0 vs 5.1: coordinate driving Hi all, Thanks to Alan Shusterman (Reed College) and Rick Barton (Wavefunction) for responding. I have summarized below. Alan has a good workaround which will work just fine for sampling a single torsion angle. However, in the problems I am analyzing I actually have the need to do single-point energies while sampling 3, 4, even 5 torsion angles all simultaneously, so I'm at a loss still as to how to handle that with SPARTAN 5.1. We are currently investigating the use of other codes to tackle this problem, including PCModel (which we just acquired). Gary Strahan (U of Maryland) also responded humorously with advice I can't agree with (for reasons stated below)...upgrading a complex package like Unix-SPARTAN is generally important to do on a regular basis. Best wishes, Robert Topper Dept of Chemistry Cooper Union New York, NY 10003 roberttopper@roberttopper.com ***************************************************************** No problem - create the molecules you want manually. Build the first molecule and use Save in the Builder to give it a name (Try01). Then, while still in the Builder, select Dihedral from the Geometry menu, select the torsion of interest, type a new value into the text box, and press Enter. This will change the dihedral without changing any other coordinates. Then use Save As to give this model a new name (Try02). Create all of the other models you need while still in the Builder. If you want, after you leave the Builder, open all of the models simultaneously, and use Group (File menu) to create a single list. Good luck, -Alan ==== Alan Shusterman Department of Chemistry Reed College Portland, OR ****************************************** ...This functionality was eliminated in Unix Spartan 5.1 and the only work around is to create a list of molecules that are individually altered by the desired incremental value or to use coordinate driving. This is the only advice I can offer currently and comes from the computational design staff. I inquired as to this functionality being available in our Spartan/Qchem product that is to be released soon. The inclusion of this functionality will be considered for the next version. Whether it will be possible to include with the new q-chem backend is another issue. Best regards, Rick Barton Customer Support Manager Wavefunction, Inc. ****************************************** I can not offer you any assistance, but you do confirm my motto about software that works: "Never upgrade!" =) (We have only an older version of SPARTAN here...) Good luck! Gary ****************************************** > From Robert: Gary's advice generally applies, but I think not in this case. Older versions of SPARTAN cannot be characterized as "software that works." SPARTAN 4.0 has some problems with some of its minimizers, and SPARTAN 5.0's implementation of MMFF94 is flawed and its density-functional theory module also had some problems. These problems are all documented in the release notes which came with the subsequent versions and / or have been reported in the CCL. Only version 5.1 is relatively bug-free in ALL of its modules (although its online documentation is somewhat less than wonderful), and version 5.1 has many computational enhancements over previous versions, including greatly enhanced speed, improved performance, and the ability to analyze many more conformers in the conformer search utility, plus some nifty little features that other codes still lack. Personally, I'm looking forward to upgrading to the next UNIX (or LINUX) version of SPARTAN when it becomes available. From chemistry-request@server.ccl.net Fri Jul 13 06:07:09 2001 Received: from medserv04.medivir.se ([193.15.239.161]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6DA78528551 for ; Fri, 13 Jul 2001 06:07:09 -0400 Received: by MEDSERV04 with Internet Mail Service (5.5.2653.19) id ; Fri, 13 Jul 2001 12:00:59 +0200 Message-ID: <056DDF2B7575D311B38B009027B1136D68EA53@MEDSERV04> From: Marcel Linschoten To: chemistry@ccl.net Subject: "Drug Design and creativity" conference, Assos Turkey, 2002 Date: Fri, 13 Jul 2001 12:00:58 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6DA7A528552 Dear colleagues, I am planning to organize a conference on the interface of (drug) design and psychology. Having worked in the field of Computer-Aided Drug Design (CADD) since 1982, my experience is still that my best ideas for novel compounds just seem to pop up at unexpected moments when I am not "officially" at work. Either during a holiday, a walk or even when I have just woken up in the morning and still somewhere between sleeping and awakening: those are the moments the best ideas come. It seems that the subconscious plays an important role in the creativity process. This is -of course- a well known fact. Everyone is familiar with Kekulé's dream on the structure of benzene (a serpent biting its own tail). An interesting question is of course how we can stimulate creativity and become better drug designers. Are there any proven ways of doing this? I would like you to come up with possible names for the organizing comittee for this conference, both creative drug designers with a proven record of success as well as reknowned psychologists who have insight in the conscious and subconscious components of creativity. I suggest Assos in Turkey (Asia Minor) as an excellent site for such a conference. Historical sites like Troy, Pergamum and Lesbos (Greece, just off the coast) are in its immediate surroundings. This conference is meant to be an interesting mix of drug design, creativity and some philosophy about the future od CADD. I am looking forward to your reactions. I will summarize your viewpoints for the CCL. regards Marcel R. Linschoten, PhD Principal Scientist Medivir AB, Lunastigen 7 ,S-141 44 Huddinge, Sweden mailto:Marcel.Linschoten@medivir.se , http://www.medivir.se tel. direct. +46-8-608 31 35, mobile +46-70-648 18 97, fax. +46-8-608 31 88 CONFIDENTIALITY NOTICE: This email transmission contains confidential or legally privileged information that is intended only for the individual or entity indicated in the email address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or reliance upon the contents of this transmission is strictly prohibited. If you have received this email in error, please reply to the sender so that Medivir can arrange for proper delivery, and then delete the message from your inbox. Thank you. From chemistry-request@server.ccl.net Fri Jul 13 03:13:11 2001 Received: from postfix1.uni-muenster.de ([128.176.188.57]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6D7DB512885 for ; Fri, 13 Jul 2001 03:13:11 -0400 Received: from cheops8c (RAS21-146.UNI-MUENSTER.DE [128.176.234.147]) by postfix1.uni-muenster.de (Postfix) with SMTP id 603A110D2 for ; Fri, 13 Jul 2001 09:12:44 +0200 (MES) Message-Id: <3.0.1.32.20010713091318.0127e224@pop.uni-muenster.de> X-Sender: jodickt@pop.uni-muenster.de X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Fri, 13 Jul 2001 09:13:18 +0200 To: chemistry@ccl.net From: Tim =?iso-8859-1?Q?J=F6dicke?= Subject: CCL: TS-Search in G98 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6D7DB512886 Hi all, i am searching for som transition states with Gaussian98, Rev. 7A., and i realized (from my own experiences and a thread in this list) that the TVector=N-Option does not work at all. Since the last mail was not summarized (and the author had not answered yet) i will ask once again: Does anyone know a workaround to force G98 to take another than the lowest eigenvalue for a transition-state searche? QST2/3 are working quite well, but it would be really nice to have a proper way of calculating TS. Thanks in advance (and i will summarize) tim ******************************************************** Tim Jödicke, Michaelweg 22, 48149 Münster 0251/869057 email: jodickt@uni-muenster.de .... my brain hurts! Terry Gilliam ******************************************************** From chemistry-request@server.ccl.net Fri Jul 13 07:02:37 2001 Received: from mail2.uniroma1.it ([151.100.4.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6DB2a531266 for ; Fri, 13 Jul 2001 07:02:37 -0400 Received: from rcmdpc450w ([151.100.64.10]) by mail2.uniroma1.it (Lotus Domino Release 5.0.8) with SMTP id 2001071313082174:2979 ; Fri, 13 Jul 2001 13:08:21 +0200 From: "Rino Ragno" To: Cc: Subject: Macromodel Magnesium parameters Date: Fri, 13 Jul 2001 13:03:45 +0200 Message-ID: MIME-Version: 1.0 X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal In-Reply-To: <200107112151.QAA13407@mole.chem.iupui.edu> X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MIMETrack: Itemize by SMTP Server on mail2/Uniroma1/it(Release 5.0.8 |June 18, 2001) at 13/07/2001 13.08.21, Serialize by Router on mail2/Uniroma1/it(Release 5.0.8 |June 18, 2001) at 13/07/2001 13.08.24, Serialize complete at 13/07/2001 13.08.24 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" MacroModel Users, I am looking for Mg amber FF parameters to be included in the amber.fld and atom.typ files and to perform some calculation on Mg containing proteins. I will summarize the aswers. 10x Rino Ragno ++-------------------------------------------------------++ || Dr. Rino Ragno || || Dip. Studi Chimica Tecnonologia Sostanze || || Biologicamente Attive || || Facolta' di Farmacia - Universita' "La Sapienza" || || P.le Aldo Moro, 5 - 00185 - Roma/Italia || || || || Phone: 39-6-49913152 (work: voice) || || Fax: 39-6-49913133 (Dipartimental) || || E-mail: rino.ragno@uniroma1.it (work) || ++-------------------------------------------------------++ From chemistry-request@server.ccl.net Thu Jul 12 18:03:38 2001 Received: from richardson.uni2.net ([129.142.7.104]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6CM3b508314 for ; Thu, 12 Jul 2001 18:03:37 -0400 Received: from fw-1a (mail.lundbeck.com [130.227.160.31]) by richardson.uni2.net (8.11.0/8.11.0) with SMTP id f6CM3aA13487 for ; Fri, 13 Jul 2001 00:03:36 +0200 Received: FROM ludk0006.lundbeck.com BY ludk0163.lundbeck.com ; Fri Jul 13 00:03:27 2001 +0200 Received: from lundbeck.com (192.168.235.211 [192.168.235.211]) by ludk0006.lundbeck.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 3ZQWNQYK; Fri, 13 Jul 2001 00:03:27 +0200 Sender: torleif@richardson.uni2.net Message-ID: <3B4E1E9E.8F627B5D@lundbeck.com> Date: Fri, 13 Jul 2001 00:03:10 +0200 From: Jan Torleif Pedersen X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: GLw - GL Widget toolkit for Linux ? Content-Type: multipart/mixed; boundary="------------12833B13712C37E27A77FA01" This is a multi-part message in MIME format. --------------12833B13712C37E27A77FA01 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------12833B13712C37E27A77FA01 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Mozilla-Status2: 00000000 Message-ID: <3B4E17C3.230093E4@torleif.org> Date: Thu, 12 Jul 2001 23:33:55 +0200 From: Jan Torleif Pedersen X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: GLw - GL Widget toolkit for Linux ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings chemists, I am in the process of rewriting an old molecular graphics toolkit and would like it to be both portable and flexible. OpenGL is an obvious chice for the molecule display, a number of integrations of OpenGL into the X windows system are available. Some integrations are smooth and use the GLU toolkit, but limited in user control. The other option is GLX which allows low level control, but does require a substantial amount of programming. A good solution appears to be the GLw or GL Widget library supplied by SGI and as far as I recall it is also avalable for IBM platforms. I have not seen any public domain GLw libraries - is anybody aware of the existence of such a toolkit for Linux ? and if so does it work with Mesa ? --- Jan Dr. Jan T. Pedersen Computational Chemistry Group H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark jatp@lundbeck.com --------------12833B13712C37E27A77FA01-- From chemistry-request@server.ccl.net Fri Jul 13 17:54:02 2001 Received: from talisker.emsl.pnl.gov ([198.128.80.38]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6DLs1507347 for ; Fri, 13 Jul 2001 17:54:01 -0400 Received: (from ng570@localhost) by talisker.emsl.pnl.gov (8.8.6 (PHNE_17135)/8.8.6) id OAA19384 for chemistry@ccl.net; Fri, 13 Jul 2001 14:53:56 -0700 (PDT) From: Kirk Peterson Message-Id: <200107132153.OAA19384@talisker.emsl.pnl.gov> Subject: CCL:TS-Search in G98 To: chemistry@ccl.net Date: Fri, 13 Jul 2001 14:53:56 -0700 (PDT) X-Mailer: ELM [Revision: 213.1] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit my apologies for perhaps the multiple posts - I'm having a rough afternoon.... :^) Tim, I came across this problem just yesterday. The fix seems to be to use the Gaussian94 approach - use internal coordinates and insert the number 10 at the end of the n'th variable definition to follow the n'th mode. Note that this mode does not have to have anything in common with this particular internal coordinate. If you want to follow a mode that is dominated by a particular internal coordinate, one puts a "4" after this variable's definition. Strange, but seems to work. regards, Kirk P.S. - Here's the G94 manual's example for the HCN --> HNC TS to follow mode 2 (the bend) # opt=(ef,ts) EF test 0 1 N C 1 cn H 1 ch 2 hcn cn=1.3 ch=1.20 10 hcn=60.0 ------------------------------------------------------------------------------ Kirk A. Peterson Associate Professor Affiliate Senior Research Scientist Department of Chemistry & Theory, Modeling, and Simulation 2710 University Dr. Environmental Molecular Sciences Laboratory Washington State University Pacific Northwest National Laboratory Richland, WA 99352 P.O. Box 999, Mail Stop K8-91 Office: (509) 376-2023, (509) 372-7282 Fax: (509) 376-0420 kirk.peterson@pnl.gov http://www.tricity.wsu.edu/~kipeters/ ------------------------------------------------------------------------------ > > > > > > > Hi all, > > > > > > i am searching for som transition states with Gaussian98, Rev. 7A., and i > > > realized (from my own experiences and a thread in this list) that the > > > TVector=N-Option does not work at all. > > > Since the last mail was not summarized (and the author had not answered > > > yet) i will ask once again: Does anyone know a workaround to force G98 to > > > take another than the lowest eigenvalue for a transition-state searche? > > > QST2/3 are working quite well, but it would be really nice to have a proper > > > way of calculating TS. > > > > > > Thanks in advance (and i will summarize) > > > > > > tim > > > ******************************************************** > > > > > > Tim Jödicke, Michaelweg 22, 48149 Münster > > > 0251/869057 > > > email: jodickt@uni-muenster.de > > > > > > .... my brain hurts! > > > Terry Gilliam > > > > > > ******************************************************** > > > > > > > > > > ----- End of forwarded message from ng570 ----- > > -- > > ------------------------------------------------------------------------------ > Kirk A. Peterson > Associate Professor Affiliate Senior Research Scientist > Department of Chemistry & Theory, Modeling, and Simulation > 2710 University Dr. Environmental Molecular Sciences Laboratory > Washington State University Pacific Northwest National Laboratory > Richland, WA 99352 P.O. Box 999, Mail Stop K8-91 > > Office: (509) 376-2023, (509) 372-7282 > Fax: (509) 376-0420 > kirk.peterson@pnl.gov > http://www.tricity.wsu.edu/~kipeters/ > ------------------------------------------------------------------------------ > ----- End of forwarded message from ng570 ----- -- ------------------------------------------------------------------------------ Kirk A. Peterson Associate Professor Affiliate Senior Research Scientist Department of Chemistry & Theory, Modeling, and Simulation 2710 University Dr. Environmental Molecular Sciences Laboratory Washington State University Pacific Northwest National Laboratory Richland, WA 99352 P.O. Box 999, Mail Stop K8-91 Office: (509) 376-2023, (509) 372-7282 Fax: (509) 376-0420 kirk.peterson@pnl.gov http://www.tricity.wsu.edu/~kipeters/ ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Jul 13 17:51:16 2001 Received: from talisker.emsl.pnl.gov ([198.128.80.38]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6DLpF507319 for ; Fri, 13 Jul 2001 17:51:15 -0400 Received: (from ng570@localhost) by talisker.emsl.pnl.gov (8.8.6 (PHNE_17135)/8.8.6) id OAA19363 for chemistry@www.ccl.net; Fri, 13 Jul 2001 14:51:09 -0700 (PDT) From: Kirk Peterson Message-Id: <200107132151.OAA19363@talisker.emsl.pnl.gov> Subject: CCL:TS-Search in G98 To: chemistry@server.ccl.net Date: Fri, 13 Jul 2001 14:51:09 -0700 (PDT) X-Mailer: ELM [Revision: 213.1] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Sorry, I had originally sent this to chemistry-request@ccl.net Tim, I came across this problem just yesterday. The fix seems to be to use the Gaussian94 approach - use internal coordinates and insert the number 10 at the end of the n'th variable definition to follow the n'th mode. Note that this mode does not have to have anything in common with this particular internal coordinate. If you want to follow a mode that is dominated by a particular internal coordinate, one puts a "4" after this variable's definition. Strange, but seems to work. regards, Kirk P.S. - Here's the G94 manual's example for the HCN --> HNC TS to follow mode 2 (the bend) # opt=(ef,ts) EF test 0 1 N C 1 cn H 1 ch 2 hcn cn=1.3 ch=1.20 10 hcn=60.0 ------------------------------------------------------------------------------ Kirk A. Peterson Associate Professor Affiliate Senior Research Scientist Department of Chemistry & Theory, Modeling, and Simulation 2710 University Dr. Environmental Molecular Sciences Laboratory Washington State University Pacific Northwest National Laboratory Richland, WA 99352 P.O. Box 999, Mail Stop K8-91 Office: (509) 376-2023, (509) 372-7282 Fax: (509) 376-0420 kirk.peterson@pnl.gov http://www.tricity.wsu.edu/~kipeters/ ------------------------------------------------------------------------------ > > > > Hi all, > > > > i am searching for som transition states with Gaussian98, Rev. 7A., and i > > realized (from my own experiences and a thread in this list) that the > > TVector=N-Option does not work at all. > > Since the last mail was not summarized (and the author had not answered > > yet) i will ask once again: Does anyone know a workaround to force G98 to > > take another than the lowest eigenvalue for a transition-state searche? > > QST2/3 are working quite well, but it would be really nice to have a proper > > way of calculating TS. > > > > Thanks in advance (and i will summarize) > > > > tim > > ******************************************************** > > > > Tim Jödicke, Michaelweg 22, 48149 Münster > > 0251/869057 > > email: jodickt@uni-muenster.de > > > > .... my brain hurts! > > Terry Gilliam > > > > ******************************************************** > > > > > ----- End of forwarded message from ng570 ----- -- ------------------------------------------------------------------------------ Kirk A. Peterson Associate Professor Affiliate Senior Research Scientist Department of Chemistry & Theory, Modeling, and Simulation 2710 University Dr. Environmental Molecular Sciences Laboratory Washington State University Pacific Northwest National Laboratory Richland, WA 99352 P.O. Box 999, Mail Stop K8-91 Office: (509) 376-2023, (509) 372-7282 Fax: (509) 376-0420 kirk.peterson@pnl.gov http://www.tricity.wsu.edu/~kipeters/ ------------------------------------------------------------------------------