From chemistry-request@ccl.net Thu Jun 10 05:49:36 2004 Received: from cholla.wustl.edu (cholla.wustl.edu [128.252.62.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AAnZc3024700 for ; Thu, 10 Jun 2004 05:49:35 -0500 Received: from cholla.wustl.edu (localhost.localdomain [127.0.0.1]) by cholla.wustl.edu (8.12.11/8.12.10) with ESMTP id i5AAraYg030240; Thu, 10 Jun 2004 05:53:36 -0500 Received: (from baker@localhost) by cholla.wustl.edu (8.12.11/8.12.11/Submit) id i5AArZjV030238; Thu, 10 Jun 2004 05:53:35 -0500 Date: Thu, 10 Jun 2004 05:53:35 -0500 From: "Nathan A. Baker" To: Warren DeLano Cc: "'Ankit Soni'" , chemistry-.at.-ccl.net, pymol-users-.at.-lists.sourceforge.net Subject: Re: CCL:How to change PDB into PDBQ using PyMOL Message-ID: <20040610105335.GG29886-.at.-cholla.wustl.edu> References: <00de01c44e90$85458740$3d501aac@iceman> <200406091807.i59I7Kjq006454-.at.-server.ccl.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <200406091807.i59I7Kjq006454-.at.-server.ccl.net> User-Agent: Mutt/1.4.1i Organization: Washington University in St. Louis X-URL: http://www.biochem.wustl.edu/~baker X-PGP-Key: http://cholla.wustl.edu/~baker/pubkey.asc X-Spam-Status: No, hits=-1.0 required=7.5 tests=X_URL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi All -- PDB2PQR (http://agave.wustl.edu/pdb2pqr) is designed to prepare input files for electrostatics calculations (add hydrogens, optimize H-bonding, assign parameters) and returns a PQR format very similar to the PDBQ format required by Autodock. This may provide the functionality you are looking for. Thanks, Nathan Warren DeLano (06-09-2004 11:06:47-0700): >Ankit, > > To my knowledge, no one has worked this out, but you might have >better luck getting an answer on the PyMOL Users mailing list, to which I've >cc'd this message. My impression is that AutoDock is facilitated using the >AutoDock tools built into PMV. > > In principle, PyMOL could become a convenient tool for preparing >input files for programs like Mead, APBS, Gromacs, Amber, etc., but that >hasn't happened yet... > >Cheers, >Warren > >> -----Original Message----- >> From: Computational Chemistry List >> [mailto:chemistry-request-.at.-ccl.net] On Behalf Of Ankit Soni >> Sent: Wednesday, June 09, 2004 7:13 PM >> To: chemistry-.at.-ccl.net >> Subject: CCL:How to change PDB into PDBQ using PyMOL >> >> HI CClers: >> >> Would someone please tell me that is PyMOL capable of >> changing PDB file into PDBQ files which can be used by >> Autodock3 ,if yes please give the procedure(steps) in detail. >> >> Thanks for the help and patience.. >> >> Sincerely, >> >> Ankit Soni > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY-.at.-ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > End of message from Warren DeLano. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc From chemistry-request@ccl.net Wed Jun 9 16:20:30 2004 Received: from web13603.mail.yahoo.com (web13603.mail.yahoo.com [216.136.175.114]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i59LKTiE019744 for ; Wed, 9 Jun 2004 16:20:29 -0500 Message-ID: <20040609212428.96537.qmail[at]web13603.mail.yahoo.com> Received: from [160.75.79.238] by web13603.mail.yahoo.com via HTTP; Wed, 09 Jun 2004 14:24:28 PDT Date: Wed, 9 Jun 2004 14:24:28 -0700 (PDT) From: Urartu "Vzg|r" "^afak" "^EKER" Subject: Modelling at the Peptide and Inorganic interface To: chemistry[at]ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello Everybody on the list, I am working on the modelling of the peptides that specifically bind to the inorganic surfaces, i am trying to create a muscovite surface using the software called HyperChem 7,5, but i cannot achieve it. Can anybody tell me how to create and optimize a mica surface. Thank you for interest and considering my question. Regards, ===== Research Asst.URARTU V.^.SEKER ]stanbul Technical University Molecular Biology and Genetics Department web: www.be.itu.edu.tr/~urartuseker email:urartuseker[at]be.itu.edu.tr __________________________________ Do you Yahoo!? Friends. Fun. Try the all-new Yahoo! Messenger. http://messenger.yahoo.com/ From chemistry-request@ccl.net Thu Jun 10 04:14:34 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5A9EY3r017381 for ; Thu, 10 Jun 2004 04:14:34 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HZ3002C75UVPN~at~mailserver.unimi.it> for chemistry~at~ccl.net; Thu, 10 Jun 2004 11:18:31 +0200 (MEST) Received: from villa.unimi.it (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HZ300KM65USB8~at~smtp.unimi.it> for chemistry~at~ccl.net; Thu, 10 Jun 2004 11:18:29 +0200 (MEST) Date: Thu, 10 Jun 2004 11:21:09 +0200 From: Giulio Vistoli Subject: Re: CCL:How to change PDB into PDBQ using PyMOL In-reply-to: <00de01c44e90$85458740$3d501aac@iceman> X-Sender: giulio.vistoli~at~mailserver.unimi.it To: Ankit Soni , chemistry~at~ccl.net Message-id: <6.1.1.1.0.20040610111934.024010e0~at~mailserver.unimi.it> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 6.1.1.1 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7BIT References: <00de01c44e90$85458740$3d501aac@iceman> Dear Ankit, VEGA (www.ddl.unimi.it) can assign atomic charges and convert PDB into PDBQ Best regards Giulio Vistoli From chemistry-request@ccl.net Thu Jun 10 01:59:44 2004 Received: from mailfilter.diszk.unideb.hu (mailfilter.diszk.unideb.hu [193.6.138.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5A6xg3r007681 for ; Thu, 10 Jun 2004 01:59:42 -0500 Received: from mailfilter.diszk.unideb.hu (localhost [127.0.0.1]) by mailfilter.diszk.unideb.hu (Postfix) with SMTP id 494AAA01DD; Thu, 10 Jun 2004 09:03:42 +0200 (CEST) Received: from Cthulhu (anti309.chem.klte.hu [193.6.133.108]) by delfin.unideb.hu (Postfix) with SMTP id 58544C809; Thu, 10 Jun 2004 09:03:41 +0200 (DFT) Message-ID: <000f01c44eb9$11a4dd30$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: "'Ankit Soni'" , References: <200406091807.i59I7Kjq006454~at~server.ccl.net> Subject: Re: CCL:How to change PDB into PDBQ using PyMOL Date: Thu, 10 Jun 2004 09:03:44 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Ankit, Among others Mol2Mol can convert to the PDBQ, Rasmol/Chime etc subformats of PDB files. Of course the starting molecule file should already contain the atomic charges. http://web.interware.hu/frenzy/mol2mol/index.html With regards Tamas Gunda tgunda *AT* puma.unideb.hu > > -----Original Message----- > > From: Computational Chemistry List > > [mailto:chemistry-request~at~ccl.net] On Behalf Of Ankit Soni > > Sent: Wednesday, June 09, 2004 7:13 PM > > To: chemistry~at~ccl.net > > Subject: CCL:How to change PDB into PDBQ using PyMOL > > > > HI CClers: > > > > Would someone please tell me that is PyMOL capable of > > changing PDB file into PDBQ files which can be used by > > Autodock3 ,if yes please give the procedure(steps) in detail. > > > > Thanks for the help and patience.. > > > > Sincerely, > > > > Ankit Soni > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY~at~ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 10 08:39:31 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5ADdUc3000862 for ; Thu, 10 Jun 2004 08:39:30 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.10) with ESMTP id i5ADeQDU031534 for ; Thu, 10 Jun 2004 10:40:26 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id i5ADhPAD013579 for ; Thu, 10 Jun 2004 10:43:25 -0300 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id i5ADhNcd013574 for chemistry/at/ccl.net; Thu, 10 Jun 2004 10:43:23 -0300 Received: from imac1.chem.unb.ca (imac1.chem.unb.ca [131.202.174.199]) by webmail.unb.ca (IMP) with HTTP for ; Thu, 10 Jun 2004 10:43:23 -0300 Message-ID: <1086875003.40c8657bb4abb/at/webmail.unb.ca> Date: Thu, 10 Jun 2004 10:43:23 -0300 From: Joe Harriman To: CCL posting Subject: Summary: correlating in silico TS energies with ee values MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.174.199 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: s808o/at/unb.ca X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Thanks for everyone for their replies. The following is a summary of the responses given to my initial question. In short I had asked if there were any methods available to correlate experimental ee values with TS energies obtained in silico. Hope this can help others as well. Hi Joe, The critical number you would need is the activation energy, i.e. the difference between the transition state energy and the reactants ground state energy (ideally free energies including the entropic term). This should correlate with the energy of activation (Ea) from the Arrhenius equation. http://www.shodor.org/UNChem/advanced/kin/arrhenius.html Then, you would need to test the correlation of the calculated activation energies with some experimentally-derived numbers to: 1) establish that the model and theory-level does reasonably reproduce your experimentally observed results 2) to create a 'calibration' equation to more accurately estimate activation energies for new reaction paths If kinetically controlled, then the product ratios should be related to the respective reaction rates. If thermodynamically controlled, then the product energies (energies of reaction) should control the product ratios. This approach has been applied in a paper by: Malwitz, N., Reaction Kinetic Modeling from PM3 Transition State Calculations, J. Phys. Chem., Vol 99, No. 15, 1995 p. 5291 Regards, David Gallagher CAChe Group, Fujitsu Portland, Oregon Hi, This comes out of the Eyring or Arrhenius equations, which you find in any basic physical chemistry text book. Arrhenius: k = A exp(-Ea/RT); I prefer Eyring, but they give the same results when you're looking at relative rates. As a first approximation assume that the constant(s) are equal for both paths (usually including the entropy, a fairly strong approximation...). I assume that you're looking at an irreversible step, then the ratio of products, r, can be obtained simply as the ratio of rate constants, r = exp(DEa/RT), where DEa is the difference in transition state energy (all the constants disappear in the division). When you have the ratio, the ee is easily obtained from ee = (r-1)/(r+1), which is the excess divided by the total, the definition of ee. /Per-Ola Joe, The enantiomeric excess can be expressed as a ratio which means that you should be able to predict the ration from using the dG values at the dtationary point (TS). At a minimum, you need to do frequency calculations in order to obtain dG values. You know that one can consider that a pair of diastereomeric transition states (and they have to be to have different TS energies as enantiomeric TS have equivalent energies) can be considered to be an equilibrium reaction so K# = exp[-DG/RT]. So you can compare TS Equilibrium constants K#(1)/K#(2) = exp[(DG(2)-DG(1))/RT] > From this it is easy to see how you could predict ration of optical isomers. I hope this helps... Mark Hi, All other things equal, the energies can be treated as classical barriers relative to the ground-state for the start of the reaction. I would calculate that as the end of an IRC run (or DRC with some handwaving), depending on the program you are using. Then use the apparent DeltaEdagger in the Arrhenius equation. Or use the delta(deltaEdagger) as a measure of the relative ratios of the isomers.This should lead (at worst) to a prediction of the predominant isomer, assuming kinetic control of the reaction. Delta(deltaE) (from the two ends of the IRC) can be used as a prediction of the predominant isomer, assuming thermodynamic control. Sb Hi, First, I am not an expert in this area, and I will be very much interested in the summary of all the answers that you will get. That said, I think that it depends on wether the two enantiomeric products are obtained under a kinetic control or under thermodynamic control. If the experimental conditions are such that you obtain the thermal equilibrium for your products then you should use their energies to calculate their proportions. (Bearing in mind that enantiomers have the same energy, then you should get ee=0.) Assuming that you are under kinetic control, I would suggest using the Transition State Theory that states that the rate constant is proportional to exp(-Delta_G(TS)/RT). Then you can see that the concentration of each product is proportionnal to k and thus to this exponential term : [A]/[B]=exp(-(Delta_G(TS-A)-Delta_G(TS-B))/RT) If you think that the entropic contribution is the same for both TS, you can write: [A]/[B]=exp(-(Delta_E(TS-A)-Delta_E(TS-B))/RT) hope this helps, Paul. Joe, Please take a look at the following publication from Ken Houk's group. I did the calculations for stereoselective hydroborating agents - mono and di-isopinanylcampheylboranes. We used a hybrid QM/MM method at that time due to the difficulty of using a complete QM approach for the system. If you read the paper and references carefully, you should see some formulas showing how to convert relative energies into enantiomeric excess values. There is also an earlier publication (of which I am a co-author) - should be Tetrahedron, or something similar listed in the Science paper. Sorry, I do not a copy of the paper with me at the moment. Contact me or Ken Houk (UCLA) if you have further questions. Regards, Jim Metz From chemistry-request@ccl.net Thu Jun 10 09:08:17 2004 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AE8Hc3002568 for ; Thu, 10 Jun 2004 09:08:17 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id i5AEAqkj025738; Thu, 10 Jun 2004 10:12:19 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.5.43) with SMTP id M2004061010121902279 ; Thu, 10 Jun 2004 10:12:19 -0400 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id i5AECJao026281; Thu, 10 Jun 2004 10:12:19 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id i5AECIP3004426; Thu, 10 Jun 2004 10:12:19 -0400 (EDT) Date: Thu, 10 Jun 2004 10:12:18 -0400 (EDT) From: Yong Liang Yang To: chemistry/at/ccl.net cc: yonyang/at/ic.sunysb.edu Subject: Autodock compile Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Dear CCL users: I am a newbie to Autodock and I have some troubles to compile the /src/autodock and /src/protonate subprogram. We do not have CC and F77 compiler so we use GNU compiler. However, when I try to compile /protonate and type " make " , it still complains can not find F77 compiler. And when I try to compile /autodock, it complains " ld32: error 33 : unresolved text symbol, operator new (unsigned) --1st reference by main.o " (I did change the corresponding part in Makefile CC=gcc before I tried to compile it). I hope computer gurus or Autodock gurus could help me fix this problem. Many thanks in advance!! Cheers Yong.L.Y ^V From chemistry-request@ccl.net Thu Jun 10 12:04:18 2004 Received: from maya.uab.es (maya.uab.es [158.109.0.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AH4GoI015041 for ; Thu, 10 Jun 2004 12:04:17 -0500 Received: from CONVERSION-DAEMON.maya.uab.es by maya.uab.es (PMDF V6.2-X20 #30859) id <0HZ300C01RJBK1_at_maya.uab.es> for chemistry_at_ccl.net; Thu, 10 Jun 2004 19:06:48 +0200 (MEST) Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by maya.uab.es (PMDF V6.2-X20 #30859) with ESMTP id <0HZ30026LRJB7S_at_maya.uab.es> for chemistry_at_ccl.net; Thu, 10 Jun 2004 19:06:47 +0200 (MEST) Received: from astult.qf.uab.es ([158.109.14.42] helo=klingon.uab.es) by klingon.uab.es with esmtp (Exim 4.30) id 1BYSkR-0006Vr-KA for chemistry_at_ccl.net; Thu, 10 Jun 2004 18:49:51 +0200 Date: Tue, 10 Jun 2003 19:09:00 +0200 From: Marc Noguera Julian Subject: Experiences with 64 bits AMD processors To: chemistry_at_ccl.net Message-id: <3EE610AC.3030300_at_klingon.uab.es> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 8BIT X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Spam-Status: No, hits=1.2 required=7.5 tests=DATE_IN_PAST_96_XX autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, we are interested in buying some more computational resources. In our group we are interested in 64 bit AMD processors, but we do not know about their compatibility. They are supposed, as AMD says, to be32 bit compatible and therefore AMD 64 bit processor should be able to run any 32 bit application. Is that true? Any experience about this will help us a lot. By the way, we are running mainly gaussian jobs, and have some other 32 bit binaries like turbomole and jaguar. We have source code license for gaussian 03. Has anyone tried to compile Gaussian 03 for a AMD 64 bit machine? Do 32 bit pentium binaries run correctly on a 64 bit processor? which is the increase on the performance? Do Turbomole and Jaguar binaries run on 64 bit AMD processors? anyone tried? Any information will be helpful. Thanks a lot Marc --------------------------- Marc Noguera Julian Thcnic Especialista de Suport a la Recerca Qummica Fisica, Universitat Autrnoma de Barcelona. Tlf: 00-34-935812173 Fax: 00-34-935812920 e-mail: marc_at_klingon.uab.es --------------------------------------- From chemistry-request@ccl.net Thu Jun 10 12:20:53 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AHKqoI015910 for ; Thu, 10 Jun 2004 12:20:52 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.6a/Switch-3.1.0) with ESMTP id i5AHOsi0008708; Thu, 10 Jun 2004 12:24:54 -0500 (EST) Received: from piwnica.com (piwnica.com [66.93.212.2]) by webmail.nd.edu (IMP) with HTTP for ; Thu, 10 Jun 2004 12:24:54 -0500 Message-ID: <1086888294.40c8996622382$at$webmail.nd.edu> Date: Thu, 10 Jun 2004 12:24:54 -0500 From: Jan K Labanowski To: chemistry$at$ccl.net Cc: jlabanow$at$nd.edu Subject: CCL will be there when I am on vacations MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 66.93.212.2 X-ND-MTA-Date: Thu, 10 Jun 2004 12:24:55 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4365 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, I need to take 10 days off and will be in Arizona with the family. It is hot there, but I may survive... While I am taking a laptop with me, I am not sure that I will be able to plug it anywhere, and if my family will actually let me do it {:-(}. The good news is that Boris Gorelik from Molecular Modelling Group, Pharmacy School, Hadassa Faculty of Medicine, The Hebrew University of Jerusalem, http: // www .md.huji.ac.il/models/group.html was so kind to do the chores of reviewing messages sent to CCL which were stopped by CCL filters for inspection. With the amount of spam hitting CCL (about 3000 a day), even if most of the spam/virus is junked by spamassassin before human sees it, it is still a dounting task for someone who did not accept it as a part of his/her life. Part of the problem is YOU (just kidding... this is what you call blame the victim) who let your computers get infected and then they send me all these viruses, warms, and offers which should be tempting for the man my age. Keep your computers safe for vacations or use another operating system (do I have to say more?...). Some other things may need to wait when I come back... Be considerate and keep your fingers crossed and pray that I do not step on the rattle-snake (actually, a few years ago I almost did...). All the best for you there... Hope you are also thinking about getting some time off... -- Jan K. Labanowski, Ph.D. Tel. (574) 631-4565 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 From chemistry-request@ccl.net Thu Jun 10 10:38:55 2004 Received: from vspw2227.email.dc ([213.140.25.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AFcroI008882 for ; Thu, 10 Jun 2004 10:38:54 -0500 Received: from VSPW2113 ([172.28.32.9]) by vspw2227.email.dc with Microsoft SMTPSVC(5.0.2195.6713); Thu, 10 Jun 2004 17:42:52 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Keto-enol tautomerism studies X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Thu, 10 Jun 2004 17:42:52 +0200 Content-Class: urn:content-classes:message Message-ID: <3578F30C8DBF04489FA7E4E563407BB40C0085^at^VSPW2113.nikemresearch.dc> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Keto-enol tautomerism studies Thread-Index: AcRBbwACpJM2bmiCR+OzyxGpng3FFQNkZ3og From: "Forlani Roberto" To: X-OriginalArrivalTime: 10 Jun 2004 15:42:52.0509 (UTC) FILETIME=[974B90D0:01C44F01] X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i5AFctoI008886 Dear CCLers, below you'll find my original question about tautomerism computational approaches and all the obtained replies. Thank you very much to all of them for their kind replies. Regards, Roberto Forlani > > I'm looking for some general references about keto-enol > tautomerism studies with different semiempirical and/or ab > initio methods (... not sure about goodness of my keywords in > article retrieval). I'm particularly interested in methods comparison. > > I'll summarize all replies. > - Andrea Klamt Robert, unfortunately I do not have real results to tell, but only some preliminary experiences: With our COSMO-RS solvation model based on BP86 DFT/COSMO calculations with TZVP basis set we were by almost 5 kcal/mol off (just comparing the total free energies of keto and enol forms in bulk liquid phases). Since this is far beyond the error of the solvation model, it must mainly be an error resulting from the DFT calculation level. Nevertheless, you will always have to take the solvation appropriately into account. Perhaps a look on COSMOtherm for this purpose. - Uko Maran Following ref. provides comaprison of semi-emp. gas phase and SCRF calculations: M. Karelson, U. Maran and A. R. Katritzky, Theoretical Study of the Keto-Enol Tautomerism in Aqueous Solutions Tetrahedron 1996, 52, 11325-11328. - From chemistry-request@ccl.net Thu Jun 10 13:18:45 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AIIjoI020335 for ; Thu, 10 Jun 2004 13:18:45 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.6a/Switch-3.1.0) with ESMTP id i5AIMlWI008006; Thu, 10 Jun 2004 13:22:47 -0500 (EST) Received: from piwnica.com (piwnica.com [66.93.212.2]) by webmail.nd.edu (IMP) with HTTP for ; Thu, 10 Jun 2004 13:22:47 -0500 Message-ID: <1086891767.40c8a6f70eb90*at*webmail.nd.edu> Date: Thu, 10 Jun 2004 13:22:47 -0500 From: Jan K Labanowski To: chemistry*at*ccl.net Cc: rbross*at*mmm.com Subject: 2nd Industrial Fluid Properties Simulation Challenge MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 66.93.212.2 X-ND-MTA-Date: Thu, 10 Jun 2004 13:22:48 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4365 Forwarded message: ------------------------------- We are pleased to announce the Second Industrial Fluid Properties Simulation Challenge (IFPSC). The second IFPSC will focus on prediction of vapor pressures and heats of vaporization, gas solubility, and enthalpies of mixing using molecular simulation techniques. The primary goal of the Industrial Fluid Properties Simulation Challenge is to obtain an in-depth and objective assessment of our current capabilities to predict thermophysical properties of industrially challenging fluids using computer simulation. Details of the contest and results of the first challenge can be found at the IFPSC website: http://www.cstl.nist.gov/FluidSimulationChallenge/ You can register at the site as a participant, an observer, or express interest in becoming one of the contest judges. We would also like to invite you to join the FLUIDSIM email distribution list (http://www.freelists.org/webpage/fluidsim) which has been created to keep you updated about the latest news regarding the Challenge. More details about FLUIDSIM (including instructions for joining) and the steps taken to protect the identities of its members are provided later in this email. In order to limit the flux of unwanted information, the organizing committee will provide all future communication about the Challenge through the IFPSC website and by email updates to registered members of FLUIDSIM. If you would like to stay in touch with the IFPSC activities, please register at the website and/or join FLUIDSIM as soon as possible. We hope you will consider your participation in the Challenge and find it an interesting and useful event. Sincerely, IFPSC Organizing Committee Questions and Answers about the Simulation Challenge and FLUIDSIM: What are the prizes? The current plan is as follows: For each of the three challenge problems, $2500 will be awarded for first place, $1500 will be awarded for second, and $1000 will be divided equally among all of the other entries that meet the minimum requirements of the Challenge. A special award of $1000 will be given to "best-in-show," the entry that performs the best among those that enter all three Challenge problems. These plans are subject to change at the discretion of the organizing committee. For example, prizes may not be awarded if the level of participation is extremely small (e.g., if there are fewer valid entries than prizes for a particular problem) or if the quality of competition is deemed to be especially poor (e.g., if all of the entries for a problem are deemed to be of poor quality and not worthy of special recognition). What are the benefits of participating? Participation in the Challenge gives you an opportunity to test your models and methods on problems that have significant industrial relevance and for which you don't know the answer ahead of time. A special session at the 2004 AIChE annual meeting will be devoted to the Challenge and offers a prime opportunity for you to highlight your work, as does the special journal issue devoted to the reporting the results of the Challenge. As mentioned in the previous section, cash prizes will be awarded to all entries that meet the minimum requirements of the Challenge. Though the organizing committee intends the Simulation Challenge to be a vehicle for engagement between industry and the top practitioners in the field of molecular simulation, it also represents a good opportunity for graduate students to gain experience and exposure (and a cash prize). If you are a graduate student and are interested in any of these benefits, talk to your advisor about entering the Challenge. I! f you are a professor or group leader, you might consider using a problem or problems from the Simulation Challenge to "initiate" new students to the world of molecular simulation. If you are teaching a graduate course in statistical mechanics, molecular modeling, molecular simulation, or another closely related field, you might consider using the Simulation Challenge as a group project for your students. When are Challenge entries due? Entries must be submitted no later than Friday, September 10, 2004. The results of the Challenge will be announced at a special session at the AIChE annual meeting in Austin, TX, in November. Who organizes the Challenge? The competition is organized by scientists from 3M, BP, Case Scientific, The Dow Chemical Company, DuPont, ExxonMobil, Mitsubishi Chemical, and the National Institute of Standards and Technology. Who can enter the Challenge? The challenge is open to researchers from academia, government laboratories, and industry not affiliated with the organizing committee. Participants must register at the web site to ensure that their proposed methodology is eligible. There are no geographical restrictions regarding eligibility, and attendance at the AIChE Annual Meeting (where the champions will be announced) is not a requirement. Who will judge the Challenge? The judging will be performed by a panel of experts in the field that will be selected by the organizing committee. What is FLUIDSIM? FLUIDSIM is an email distribution list that has been created to allow timely communication of information regarding the Simulation Challenge. Who should join FLUIDSIM? The membership of the FLUIDSIM email list is intended to include both those individuals who plan to participate in the 2004 Simulation Challenge (either as a contestant or judge) AND any other individuals who are interested in molecular simulation and its use in predicting physical properties. Therefore, if you have any interest whatsoever in this area, we encourage you to join the list. You can then be kept informed about the Challenge even if you don't currently plan to actively participate. You can always unsubscribe from the email list at a later date if you desire to do so. How do I join FLUIDSIM? FLUIDSIM is strictly an "opt-in" email list. That is, if you don't want to be a part of the email list, you can simply ignore this invitation. If you do want to join, send an email to fluidsim-request*at*freelists.org and put "subscribe" (without the quotes) in the Subject line of the email. You will then automatically receive a reply email with instructions how to confirm your membership. You can also join by browsing to the list web site (http://www.freelists.org/webpage/fluidsim) and submitting the web form. If you have problems subscribing or have any other questions, please send email to info*at*fluidsim.org. What about my privacy? Will I receive spam as a result of joining FLUIDSIM? The number of emails that you will receive as a member of FLUIDSIM will be minimal (perhaps on the order of 1 per month). It is a "newsletter" type email list, so you will only receive emails from the organizing committee of the Simulation Challenge, not from the other members of the distribution list. The content of emails sent via the list will be related to the Simulation Challenge and will be text-only (no attachments). The list of members is only available to the IFPSC organizing committee. What sort of information should I expect to receive via FLUIDSIM? Information related to the Industrial Fluid Properties Simulation Challenge (e.g., an email providing notification that the Frequently Asked Questions (FAQ) page on the contest web site has been updated with new information). Feedback The organizing committee solicits your feedback. Please let us know what you think about Challenge. Suggest good problems for future Challenges. Suggest ways that the Challenge can be improved. If you don't plan to participate in the Challenge, please let us know why not and give us ideas about how you might be motivated to participate. Please send feedback to: feedback*at*fluidsim.org The Organizing Committee Raymond Mountain - NIST - chair Fiona Case - Case Scientific Anne Chaka - NIST Daniel Friend - NIST Dave Frurip - The Dow Chemical Company Joseph Golab - BP Amoco Chemical Company Peter Gordon - ExxonMobil Russ Johnson - NIST Petr Kolar - Mitsubishi Chemical Corporation Jonathan Moore - The Dow Chemical Company Jim Olson - The Dow Chemical Company Rick Ross - 3M Company Martin Schiller - DuPont From chemistry-request@ccl.net Thu Jun 10 13:34:29 2004 Received: from smtp.ucla.edu (smtp.ucla.edu [169.232.47.136]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AIYSUc021392 for ; Thu, 10 Jun 2004 13:34:28 -0500 Received: from mail.ucla.edu (mail.ucla.edu [169.232.47.135]) by smtp.ucla.edu (8.12.11/8.12.11) with ESMTP id i5AIcTiY015673; Thu, 10 Jun 2004 11:38:29 -0700 Received: from [128.97.82.155] (Yynode01.seas.ucla.edu [128.97.82.155]) (authenticated bits=0) by mail.ucla.edu (8.12.11/8.12.11) with ESMTP id i5AIcTFM003441; Thu, 10 Jun 2004 11:38:29 -0700 Message-ID: <40C8AABF.6060305-.at.-ucla.edu> Date: Thu, 10 Jun 2004 11:38:55 -0700 From: Douglas Sievers User-Agent: Mozilla Thunderbird 0.6 (X11/20040519) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Marc Noguera Julian CC: chemistry-.at.-ccl.net Subject: Re: CCL:Experiences with 64 bits AMD processors References: <3EE610AC.3030300-.at.-klingon.uab.es> In-Reply-To: <3EE610AC.3030300-.at.-klingon.uab.es> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Probable-Spam: no X-Spam-Hits: 0 X-Scanned-By: vscan.smtp.ucla.edu X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Marc, I'll point you to an earlier message about this, which was a summary of my similar question. http://www.ccl.net/cgi-bin/ccl/message.cgi?2004+04+28+013 You should also note that there is a new Gaussian 03 Revision C1, which includes Opteron support. For more info see the Gaussian website at www.gaussian.com I have run a test job or two on my Athlon64 3400+ machine, using Intel/AMD 32-bit G'03 binaries with no problems. Doug Sievers Marc Noguera Julian wrote: > Hello, > we are interested in buying some more computational resources. In our > group we are interested in 64 bit AMD processors, but we do not know > about their compatibility. They are supposed, as AMD says, to be32 > bit compatible and therefore AMD 64 bit processor should be able to > run any 32 bit application. Is that true? Any experience about this > will help us a lot. > By the way, we are running mainly gaussian jobs, and have some other > 32 bit binaries like turbomole and jaguar. We have source code license > for gaussian 03. Has anyone tried to compile Gaussian 03 for a AMD 64 > bit machine? Do 32 bit pentium binaries run correctly on a 64 bit > processor? which is the increase on the performance? Do Turbomole and > Jaguar binaries run on 64 bit AMD processors? anyone tried? > Any information will be helpful. > Thanks a lot > Marc > > --------------------------- > Marc Noguera Julian > Thcnic Especialista de Suport a la Recerca > Qummica Fisica, Universitat Autrnoma de Barcelona. > Tlf: 00-34-935812173 > Fax: 00-34-935812920 > e-mail: marc-.at.-klingon.uab.es > --------------------------------------- > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY-.at.-ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST-.at.-ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 10 13:35:05 2004 Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.134]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AIZ4Uc021435 for ; Thu, 10 Jun 2004 13:35:05 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout1.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i5AId2QG013985 for ; Thu, 10 Jun 2004 11:39:06 -0700 Received: from u.washington.edu (D-128-95-235-217.dhcp4.washington.edu [128.95.235.217]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i5AId28A029762 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 10 Jun 2004 11:39:02 -0700 Message-ID: <40C8AAC8.4090008[at]u.washington.edu> Date: Thu, 10 Jun 2004 11:39:04 -0700 From: Oliver Hucke Reply-To: ohucke[at]u.washington.edu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: binding energy of Zn2+ ligands Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'ers, I am looking for literature describing the influence of the basicity of metal ion ligands (ideally Zn2+ ligands) on the binding energy. For example, I would expect the binding energy for an imidazole to be more favorable than for an imidazole with an electron withdrawing substituent, let's say an -SO2-group. Can somebody point me to articles on this matter? Thanks a lot in advance, Oliver -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke[at]u.washington.edu _______________________________________________________________ From chemistry-request@ccl.net Thu Jun 10 14:28:04 2004 Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.uh.edu [129.7.238.204]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AJS1Uc024903 for ; Thu, 10 Jun 2004 14:28:01 -0500 Received: by nyssa.bchs.uh.edu (Postfix, from userid 1000) id A4B059E800B; Thu, 10 Jun 2004 14:26:26 -0400 (EDT) From: Jerry Ebalunode Reply-To: jebalunode*at*adrik.bchs.uh.edu Organization: University of Houston To: jebalunode*at*nyssa.bchs.uh.edu Subject: Re: CCL:Experiences with 64 bits AMD processors Date: Thu, 10 Jun 2004 14:26:26 -0400 User-Agent: KMail/1.6.2 References: <3EE610AC.3030300*at*klingon.uab.es> In-Reply-To: <3EE610AC.3030300*at*klingon.uab.es> MIME-Version: 1.0 Content-Disposition: inline Cc: chemistry*at*ccl.net Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Message-Id: <200406101426.26492.jebalunode*at*uh.edu> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Yes, 32 bit binaries will run on these chips, assuming that you are using and running your linux OS in 64 bit mode. The catch is that you need the following 1. a. Your 64 bit kernel should be built to support 32 codes (This is done by enabling the 32 bit emulation flag when configuring your linux 2.6 kernel b. Note amd64 is deprecated on 2.4 linux kernels 2.a. You need to install base emulation libraries for running 32bit x86 on amd64. These include the gibc in 32 bits You need to install X11R6 emulation libraries for running 32bit x86 X-window applications on amd64. 3. If you want to compile 32 binaries you need to also enable multi lib version of gcc (i.e. supports building of both 32 and 64 bit codes Pleas note that emulation does not imply that the code is slower on amd64, infact that same binary running in amd64 architecture out performs the same binary running in a 2.8 Ghz Pentium 4 linux box. These information is based on what I had to do to enable 32 bit support in my Gentoo linux box (amd64 3200+) which I built to run in 64 bit mode If you are interested in gentoo linux and in running 32 and 64 bit codes simulataneously see http://www.gentoo.org/proj/en/base/amd64/technotes.xml inOn Tuesday 10 June 2003 01:09 pm, you wrote: > Hello, > we are interested in buying some more computational resources. In our > group we are interested in 64 bit AMD processors, but we do not know > about their compatibility. They are supposed, as AMD says, to be32 bit > compatible and therefore AMD 64 bit processor should be able to run any > 32 bit application. Is that true? Any experience about this will help us > a lot. > By the way, we are running mainly gaussian jobs, and have some other 32 > bit binaries like turbomole and jaguar. We have source code license for > gaussian 03. Has anyone tried to compile Gaussian 03 for a AMD 64 bit > machine? Do 32 bit pentium binaries run correctly on a 64 bit processor? > which is the increase on the performance? Do Turbomole and Jaguar > binaries run on 64 bit AMD processors? anyone tried? > Any information will be helpful. > Thanks a lot > Marc > > --------------------------- > Marc Noguera Julian > Thcnic Especialista de Suport a la Recerca > Qummica Fisica, Universitat Autrnoma de Barcelona. > Tlf: 00-34-935812173 > Fax: 00-34-935812920 > e-mail: marc*at*klingon.uab.es > --------------------------------------- > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Jerry Ebalunode Ph.D. Candidate RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Thu Jun 10 19:15:35 2004 Received: from qcmm9 ([202.103.38.172]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5B0FVUc002890 for ; Thu, 10 Jun 2004 19:15:33 -0500 Received: from 163.com (qcmm9 [10.10.1.9]) by qcmm9 (8.12.8/8.12.8) with ESMTP id i5B0GxG5025937; Fri, 11 Jun 2004 08:17:00 +0800 Message-ID: <40C8F9FA.9000902*at*163.com> Date: Fri, 11 Jun 2004 08:16:58 +0800 From: scopio User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: Yong Liang Yang CC: chemistry*at*ccl.net Subject: Re: CCL:Autodock compile References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Yang You need g++ to compile autodock. You can replace your C++ part in your makefile with the following: ---------- CC = pgCC # change this to g++ LIB = -lm CSTD = -DHPPA $(PROF) $(DBUG) $(WARN) CFLAGS = $(OPT) OPTLEVEL = -O3 OPT = $(CSTD) $(OPTLEVEL) OLIMIT = $(OPT) LINKOPT = $(OPT) LINK = $(LINKOPT) LINT = lint LINTFLAGS = -DHPPA $(LIB) -c DBUG = -DNDEBUG # No debugging and no assert code PROF = # No profiling WARN = # Default warning level --------------- If this can't pass compliation, you can try ifc8.0. Good Luck! Liu Yong Liang Yang wrote: > > Dear CCL users: > > I am a newbie to Autodock and I have some troubles to compile > the /src/autodock and /src/protonate subprogram. We do not have > CC and F77 compiler so we use GNU compiler. However, when I try > to compile /protonate and type " make " , it still complains can > not find F77 compiler. And when I try to compile /autodock, it complains > " ld32: error 33 : unresolved text symbol, operator new (unsigned) > --1st reference by main.o " (I did change the corresponding part in > Makefile CC=gcc before I tried to compile it). I hope computer gurus > or Autodock gurus could help me fix this problem. Many thanks in > advance!! > > > Cheers > > > > Yong.L.Y > > > ^V > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > From chemistry-request@ccl.net Thu Jun 10 14:46:03 2004 Received: from calmail-cr.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5AJk2Uc026089 for ; Thu, 10 Jun 2004 14:46:03 -0500 Received: from [128.32.198.91] (account shaji(at)calmail.berkeley.edu HELO berkeley.edu) by calmail-cr.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP-TLS id 38194452 for chemistry(at)ccl.net; Thu, 10 Jun 2004 12:50:05 -0700 Message-ID: <40C8BB6D.20403(at)berkeley.edu> Date: Thu, 10 Jun 2004 12:50:05 -0700 From: Shaji Chempath User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: ccl Subject: IRC following in G03 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello CCLers: I am trying to follow the reaction coordinate to check whether my TST is correct or not. Using Gaussian-03 on a linux lcuster. My runs stop with a "open-new-file" written at then end of the output file (after finding 46 points on the path) any of you seen this before? any idea what this means? Thank you very much Shaji MY INPUT FILE: --------------------------------------------------------------------- %chk=irc #p B3LYP/Gen pseudo=read irc=(rcfc,forward,maxpoints=100,stepsize=3) geom=check nosymm > from a-jtst using gaussian 0 1 -H 0 6-31G* **** -S 0 6-31G* **** -O 0 6-31G* **** -C 0 6-31G* **** -Pd 0 LANL2DZ **** -Pd 1 LANL2DZ --------------------------------------------------------------------- LAST FEW LINES OF OUTPUT: --------------------------------------------------------------------- Compute integral first derivatives. ... and contract with generalized density number 0. 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 2211 NPrTT= 15662 LenC2= 1967 LenP2D= 8654. LDataN: DoStor=F MaxTD1= 6 Len= 172 LDataN: DoStor=T MaxTD1= 6 Len= 172 Leave Link 701 at Thu Jun 10 03:30:51 2004, MaxMem= 6291456 cpu: 3.2 fname=/scr/Gau-26495.d2e fd = -1 open-new-file ----------------------------------------------------------------------