From denis@messiaen.scf.fundp.ac.be Tue Nov 8 03:24:43 1994 Received: from hermes.fundp.ac.be for denis@messiaen.scf.fundp.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA05287; Tue, 8 Nov 1994 03:08:43 -0500 Received: by hermes.fundp.ac.be; id AA18860; Tue, 8 Nov 1994 09:13:20 +0100 Received: from messiaen.scf.fundp.ac.be by hermes.fundp.ac.be; id AA18860; Tue, 8 Nov 1994 09:13:20 +0100 Received: by messiaen.scf.fundp.ac.be (AIX 3.2/UCB 5.64/4.03) id AA31535; Tue, 8 Nov 1994 09:00:37 +0100 From: denis@messiaen.scf.fundp.ac.be (Jean-Pierre Denis) Message-Id: <9411080800.AA31535@messiaen.scf.fundp.ac.be> To: "Stavrev Krassimir" Cc: chemistry@ccl.net, denis@messiaen.scf.fundp.ac.be Subject: Re: CCL:Mac software inquiry In-Reply-To: (Your message of Mon, 07 Nov 94 09:15:41 EST.) <9411071415.AA21456@crunch> Date: Tue, 08 Nov 94 09:00:37 +0100 Dear Netter, What you can do is to place your binary file in a Compact Pro document, after saving it you can segment this archive on your own, e.a. segment it for D.D., H.D. diskettes or other blok size. Grettings. Jean-Pierre DENIS denis@scf.fundp.ac.be From toukie@zui.unizh.ch Tue Nov 8 04:24:43 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id DAA05550; Tue, 8 Nov 1994 03:36:53 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA04509; Tue, 8 Nov 94 09:36:51 +0100 X-Nupop-Charset: British Date: Tue, 8 Nov 1994 09:31:05 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <34266.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Oxidisability of phenolics Dear Colleagues; For a study in progress I need to have quantitative data about the "oxidisability" of various mono- and disubstituted phenolic compounds, pre- ferably at room or physiological temperature and at ca. physiological pH (i.e., ca. pH 7). Can anyone recommend a compendium or source of such data? I found a 1982 book called "The Encyclopaedia of Chemical Electrode Po- tentials" (authors: Antelman & Harris) listing EMF values for some monobasic phenols. According to this book, "The OH- reactions are considered to be at a pH of 11, other reactions in the absence of the H ion are considered to have a pH of 7, and those involving the H ion a pH of 11. Those involving both H+ and OH- can be construed to occur at a pH of 7." Considering the above, can anyone recommend a way of converting the values on pp. 244-245 of this book to EMF values for pH 7 and 37oC? Finally, some of the phenolics in which we are interested are not listed in "The Encyclopaedia of Chemical Electrode Potentials". Is there a way of theoretically calculating them? I have at my disposal the semi-empirical QM programme "MOPAC 6.0". I thank all responders in advance for generously sharing their thoughts and ideas with me. Yours sincerely, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From ARILAHTI@finabo.abo.fi Tue Nov 8 08:24:45 1994 Received: from SILKE.ABO.FI for ARILAHTI@finabo.abo.fi by www.ccl.net (8.6.9/930601.1506) id HAA06620; Tue, 8 Nov 1994 07:28:39 -0500 From: Received: from finabo.abo.fi by finabo.abo.fi (PMDF V4.3-8 #7828) id <01HJ8N8DHA80CCK77N@finabo.abo.fi>; Tue, 8 Nov 1994 14:28:15 EET Date: Tue, 08 Nov 1994 14:28:15 +0200 (EET) Subject: Summary on multiple MOPAC runs To: chemistry@ccl.net Message-id: <01HJ8N8DKRLUCCK77N@finabo.abo.fi> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT For some time ago, I asked for help in how to make only one MOPAC run at a time in a sequence of MOPAC runs. Here comes the summary. Thanks to everybody who responded. regards --ari ---------------------------------------------------------- Ari Lahti, M.D., M.Sc. Dept. Phys. Chem. Abo Akademi University Porthansg. 4-6 FIN-20500 Abo Finland tel.: 358-21-654617 fax:* 358-21-654706 e-mail: arilahti@abo.fi ---------------------------------------------------------- From: aiba@volta.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& ..the best solution turned to be what I really disliked: to call operating system from FORTRAN program. This allows you to NOT care about any queues, for FORTRAN proceeds operator by operator. For UNIX the tool is UNIX FORTRAN function "system". The lines in the FORTRAN program look like: INTEGER ISTAT CHARACTER COMMAND*(80) .... COMMAND='here is an appropriate UNIX command' ISTAT=SYSTEM(COMMAND) and you can put as many UNIX commands as you want just call SYSTEM(..) again and again with new commands inside. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& So, the overall FORTRAN program goes ONCE into a normal batch queue. Important is this: the calls for your MOPAC runs are successive because FORTRAN waits till the previous operator has been completed. So, you would have only one MOPAC at time! Is this what you needed ? Best regards and wish you success! ---------------------------------------------------------- From: soperpd@nylon.es.dupont.com (Paul D. Soper) Ari, I have one solution for this problem. I generate the .csh file for the job by simply telling MOPAC not to start running immediately. Each of these .csh files is copied to a directory used only for job control. A file named job_list is created which has one .csh file name per line. A script called run_next then... 1) Takes the first line (file name) from job_list 2) Adds some lines to the end of the file so it will execute run_next when it is done 3) Submits the modifed .csh file to the batch processing system This is run_next: #!/bin/csh set home_dir = `pwd` while (1 == 1) if (! -e job_list) then echo "job_list not found on" `date +"%D at %T"` >> job_history.txt break endif if (-z job_list) then echo "job_list empty on" `date +"%D at %T"` >> job_history.txt break endif set job = `head -1 job_list` tail +2 job_list > list.tmp mv list.tmp job_list if (! -e $job) then echo "$job not found on" `date +" %D at %T"` >> job_history.txt else if (-z $job) then echo "$job empty on" `date +" %D at %T"` >> job_history.txt else echo "## The rest of this deck was added by the user" >> $job echo "" >> $job echo "cd $home_dir" >> $job echo 'echo '"$job"' `date +" ended on %D at %T"` >> job_history.txt' >> $job echo "run_next" >> $job echo "" >> $job echo "$job" `date +" begun on %D at %T "` `bsub -q parallel $job` >> job_history.txt break endif end exit I hope this gives you some ideas. Good luck, Paul ---------------------------------------------------------- From: jxh@biosym.com (Joerg Hill) If I need to wait for a job to complete I use the following script: ----------------------------- waitforjob ------------------------------ # procedure which waits for termination of process with process id $1 if [ "$1" != "" ] then jobid=$1 else # no jobid means big sleep jobid=1 fi echo waiting for process $jobid while [ `ps -p $jobid | wc -l` -gt 1 ] do sleep 120 done --------------------------------- EOF ---------------------------------- Use it with the process ID of the job you are waiting for as parameter. Joerg-R. Hill ---------------------------------------------------------- From: "Dr. Daniel L. Severance" Hi, I'm not sure what's in the MOPAC batch script, but you could modify it to submit the job using the UNIX batch command. The file /usr/lib/cron/queuedefs contains a line like: b.2j2n90w which tells the UNIX batch command to only allow 2jobs to run at a time (2j) and give them a nice value of 2 (2n) and wait 90 seconds between checking to see if one of the running jobs is finished before submitting another (90w). Every 90secs it checks to see if a slot is open, then goes back to sleep for another 90 secs. until it finds that one job has finished. To use batch in your script just put the string: /bin/batch < Reply to: RE>CCL:MOPAC necessarily batch? Hi, I saw your message. Appended is some notes I made for myself when I set up MOPAC93 at my former place of work. I think they confirm your conclusion: ------------------------------------- 4. To use the submit-command To stack mopac93 jobs up - just type submit and the file will be added to a .qjob file in $mopacdir. *************************** SOME THINGS TO NOTE ************ ************* i) Do not run the mopac shell-script as a background process (&) ii) If you run mopac93 from a script file you will have to put the line 'source $mopacdir/mopac93.csh' at the top. iii) DO NOT stagger jobs in a script file; they will all run concurrently. iv) To stagger jobs use the "submit" command. v) Peculiarity of data-set names: NO "." - Your dataset root names may not contain a period (.) - use underscore (_) or hyphen (-) instead. Richard Bone ---------------------------------------------------------- From jkl@ccl.net Tue Nov 8 09:24:58 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA07954; Tue, 8 Nov 1994 09:19:08 -0500 Date: Tue, 8 Nov 1994 09:19:08 -0500 From: Jan Labanowski Message-Id: <199411081419.JAA07954@www.ccl.net> To: chemistry@ccl.net Subject: ACES II Workshop at OSC Cc: jkl@ccl.net Dear Netters, There is still place for 3 more participants to the ACES II (Advanced Concepts in Electronic Structure) Hands-On Workshop organized jointly by Quantum Theory Project at University of Floryda and Ohio Supercomputer Center. Date: Dec. 9-10, 1994, Place: Columbus, Ohio. The deadline for registrations is Nov. 15th. You can register by e-mail. More information about the workshop can be retrieved via e-mail by sending select chemistry get info/aces2.workshop quit to MAILSERV@ccl.net. By gopher (gopher www.ccl.net 73): info, aces2.workshop, and via WWW: http://www.ccl.net/aces2-workshop.html Hurry, since such intensive workshops are not organized frequently. Jan Labanowski jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From ANWAR@vms.huji.ac.il Tue Nov 8 10:24:50 1994 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id JAA08265; Tue, 8 Nov 1994 09:25:27 -0500 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 16:25:47 +0200 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 15:30:58 +0200 Date: Tue, 8 Nov 94 15:30 +0200 Message-id: <08110094153035@HUJIVMS> From: To: CHEMISTRY@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: ENZYMATIC REACTION Dear Netters, I would like to know if somebody encountered this kink of situation: activation energy in an enzymatic hydrolysis reaction whichmwas over 25 Kcal/mol (Experimental measurement). Thanks to all in advance. Anwar Rayan E-mail: anwar@vms.huji.ac.il From peeter@chem.ut.ee Tue Nov 8 10:32:16 1994 Received: from Tera for peeter@chem.ut.ee by www.ccl.net (8.6.9/930601.1506) id JAA09379; Tue, 8 Nov 1994 09:55:48 -0500 Received: by Tera (Linux Smail3.1.28.1 #1) id m0r4rzI-00028pC; Tue, 8 Nov 94 16:57 EET Message-Id: From: peeter@chem.ut.ee (Peeter Burk) Subject: Cadpack: where and how? To: chemistry@ccl.net Date: Tue, 8 Nov 1994 16:57:32 +0200 (EET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 525 Dear all, I am interested in program package CADPACK. How can one obtain a copy of it? How much does it cost? How can I contact people, who maintain/sell/distribute it? Please replay directly to me and I will summarise for net. Best regards, Peeter -- Peeter Burk, Ph.D. Jakobi 2, EE2400 Tartu, Estonia Institute of Chemical Physics Phone (372-7) 441-453 Tartu University Fax (372-7) 441-453 Estonia E-mail peeter@chem.ut.ee From noy@tci005.uibk.ac.at Tue Nov 8 11:25:22 1994 Received: from uibk.ac.at for noy@tci005.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id LAA10760; Tue, 8 Nov 1994 11:22:06 -0500 Received: from tci005.uibk.ac.at by uibk.ac.at with SMTP id AA26108 (5.65c/IDA-1.4.4 for ); Tue, 8 Nov 1994 17:21:44 +0100 Received: by tci005.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA21676; Tue, 8 Nov 1994 17:21:40 +0100 From: noy@tci005.uibk.ac.at (Noy) Message-Id: <9411081621.AA21676@tci005.uibk.ac.at> Subject: MD or MC To: chemistry@ccl.net Date: Tue, 8 Nov 1994 17:21:40 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1377 Dear CCL readers, I still remember the earlier time when I just started coming into the computer simulation field, observing colleagues running molecular dynamics and Monte Carlo program. I was so surprised that MD could collect many picoseconds in a day (some finished in an hour on IBM RS6000) while another mate stopped his MC in a week. Unfortunately, more CPU time doesn't mean more results and the dynamic properties owe its availability to MD. Which one, MD or MC, you will select if CPU time-constraint is imposed ? Both methods explore the phase space but MD seems to go ahead much faster. If the efficiency is one thing to think about MD is preferred since it never rejects the configuration. What is the advantage of MC and this should explain its survival through the year 2000. take care, Teerakiat --------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci5.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs --------------------------------------------------------------------------- *** I still remember that night in Bangkok. From ANWAR@vms.huji.ac.il Tue Nov 8 12:25:07 1994 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id LAA11072; Tue, 8 Nov 1994 11:43:42 -0500 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 18:43:46 +0200 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 15:30:58 +0200 Date: Tue, 8 Nov 94 15:30 +0200 Message-id: <08110094153035@HUJIVMS> From: To: CHEMISTRY@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: ENZYMATIC REACTION Dear Netters, I would like to know if somebody encountered this kink of situation: activation energy in an enzymatic hydrolysis reaction whichmwas over 25 Kcal/mol (Experimental measurement). Thanks to all in advance. Anwar Rayan E-mail: anwar@vms.huji.ac.il From jig@qorg.unizar.es Tue Nov 8 12:34:23 1994 Received: from qorg.unizar.es for jig@qorg.unizar.es by www.ccl.net (8.6.9/930601.1506) id MAA11643; Tue, 8 Nov 1994 12:22:32 -0500 Message-Id: <199411081722.MAA11643@www.ccl.net> Received: by qorg.unizar.es (1.37.109.4/16.2) id AA27225; Tue, 8 Nov 94 18:21:12 GMT From: Jose Ignacio Garcia Subject: DeFT: Basis sets for Sulfur To: chemistry@ccl.net Date: Tue, 8 Nov 94 18:21:09 MET Mailer: Elm [revision: 70.85] Dear netters, I am using the StAmant's DeFT program to calculate some heterocyclic molecules. This program contains DFT optimized basis sets only for first-row atoms. Now I intend to calculate some sulfur-containing heterocycles, and I am seeking for suitable basis sets to be used with this software. I know that conventional ab initio basis sets, such as the popular Pople ones, can be also used with DeFT in lieu of the built-in orbital basis sets, but I do not know how the necessary auxiliary basis set have to be constructed. Can anyone to point me to a reference, ftp-site, etc. where find suitable basis sets for Sulfur to be used in DFT calculations? Otherwise, how could I to construct the auxiliary basis sets for this atom? Cheers, Jose Ignacio From hinsenk@ERE.UMontreal.CA Tue Nov 8 12:39:47 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id MAA11288; Tue, 8 Nov 1994 12:00:06 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA11215 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Tue, 8 Nov 1994 11:57:22 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA16261; Tue, 8 Nov 94 11:57:21 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA08549; Tue, 8 Nov 94 11:57:20 -0500 Date: Tue, 8 Nov 94 11:57:20 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9411081657.AA08549@cyclone.ERE.UMontreal.CA> To: noy@tci005.uibk.ac.at Cc: chemistry@ccl.net In-Reply-To: <9411081621.AA21676@tci005.uibk.ac.at> (noy@tci005.uibk.ac.at) Subject: Re: CCL:MD or MC Teerakiat Kerdcharoen wrote: Which one, MD or MC, you will select if CPU time-constraint is imposed ? Both methods explore the phase space but MD seems to go ahead much faster. If the efficiency is one thing to think about MD is preferred since it never rejects the configuration. What is the advantage of MC and this should explain its survival through the year 2000. The choice between MD and MC depends not on your CPU time allocation, but on the problem you want to solve. Sometimes you don't have a choice; e.g. if your system doesn't observe Newtonian mechanics, you have to use MC (or some other appropriate technique, depending on the problem). Sometimes MD is inefficient, e.g. because it samples too small a region of phase space (which, by the way, has nothing to do with rejecting configurations or not). You might also choose MC because a special efficient MC technique is available for your problem. I'd recommend to read some books on MC techniques; they will show you what MC is good for. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From ANWAR@vms.huji.ac.il Tue Nov 8 13:26:12 1994 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id MAA11943; Tue, 8 Nov 1994 12:32:03 -0500 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 19:32:07 +0200 Received: by HUJIVMS (HUyMail-V7); Tue, 08 Nov 94 19:31:48 +0200 Date: Tue, 8 Nov 94 15:30 +0200 Message-id: <08110094153035@HUJIVMS> From: To: CHEMISTRY@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: ENZYMATIC REACTION Dear Netters, I would like to know if somebody encountered this kink of situation: activation energy in an enzymatic hydrolysis reaction whichmwas over 25 Kcal/mol (Experimental measurement). Thanks to all in advance. Anwar Rayan E-mail: anwar@vms.huji.ac.il From mensa@med.unc.edu Tue Nov 8 14:24:58 1994 Received: from med.unc.edu for mensa@med.unc.edu by www.ccl.net (8.6.9/930601.1506) id NAA13547; Tue, 8 Nov 1994 13:51:48 -0500 Received: from naples.med.unc.edu by med.unc.edu (4.1/SMI-4.0-ACB-1.0) id AA26853; Tue, 8 Nov 94 13:51:48 EST Received: by naples.med.unc.edu (4.1/SMI-4.1) id AA03031; Tue, 8 Nov 94 13:51:43 EST Date: Tue, 8 Nov 94 13:51:43 EST From: mensa@med.unc.edu (Adriana C. Vidal) Message-Id: <9411081851.AA03031@naples.med.unc.edu> To: chemistry@ccl.net Subject: Sybyl Biopolymer Loop Search users When I run Sybyl (version 6.0) Biopolymer Loop Search for a given sequence gap, I obtain -as expected- a set of loops ranking from lowest to highest RMS values. The manual suggests to choose the loop #1, i.e. lower RMS value. But in some cases, loops #1 have negative homology values. Does anyone know which homology matrix is the program using, besides the pmutation one? And, is one suppose to pick loop #1 regardless the negative homology value? I will much appreciate your help, Adriana C. Vidal mensa@med.unc.edu From h.rzepa@ic.ac.uk Tue Nov 8 15:24:56 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id PAA15184; Tue, 8 Nov 1994 15:17:30 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <11146-0@punch.ic.ac.uk>; Tue, 8 Nov 1994 18:01:09 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA11619; Tue, 8 Nov 94 18:01:10 GMT X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 8 Nov 1994 18:01:12 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: Announce Rasmol 2.5 for X, Windows and Mac On behalf of Roger Sayle, the availability of RasMol for X-Window, MS Window and Macintosh platforms is announced. It is available by anon ftp from ftp.dcs.ed.ac.uk in pub/rasmol If you dont know it already, this is VERY fast pdb, xyz, and other format molecular renderer. It has a sophisticated selection and attribute syntax, and can produce ribbon displays etc. It can be compiled as 8-bit or 32-bit, for those machines that support 24-bit graphics. Dr Henry Rzepa, Department of Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.1.1, Tel (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804. World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html From ZUILHOF@CHEM.CHEM.ROCHESTER.EDU Tue Nov 8 15:29:43 1994 Received: from chem.chem.rochester.edu for ZUILHOF@CHEM.CHEM.ROCHESTER.EDU by www.ccl.net (8.6.9/930601.1506) id OAA14984; Tue, 8 Nov 1994 14:59:35 -0500 From: Received: from CHEM.CHEM.ROCHESTER.EDU by CHEM.CHEM.ROCHESTER.EDU (PMDF V4.2-14 #6313) id <01HJ8QENK7X00008XT@CHEM.CHEM.ROCHESTER.EDU>; Tue, 8 Nov 1994 15:56:16 EDT Date: Tue, 08 Nov 1994 15:56:15 -0400 (EDT) Subject: Summary: UHF vs ROHF in semiempirical calc's of radical cations To: chemistry@ccl.net Message-id: <01HJ8QENK7X20008XT@CHEM.CHEM.ROCHESTER.EDU> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: ZUILHOF MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCl'ers, As promised I hereby send you the summary of all responses I received on my questions about the use of ROHF versus UHF in semiempirical calculations of radical cations. This summary starts with the original posting, followed by the responses. A big THANKS to all those who responded! Han Zuilhof ############################################################################## Original posting: Subj: ROHF versus UHF in semiempirical calc.'s of radical cations Dear CCl'ers, Semiempirical programs such as MOPAC allow the properties of radicals and radical ions to be calculated with both the Restricted Open-shell Hartree-Fock method (ROHF) and the Unrestricted Hartree-Fock (UHF) methods. I want to calculate reactionpaths for nucleophilic attack on a series of radical cations. Does anyone know of 1) any apriori reasons why one method might be preferred over the other in such calculations? 2) literature data in which the performance of the ROHF and UHF methods for the study of radical cations is compared directly? Please report directly to me, and I'll summarize to the net. Thanks in advance, Han Zuilhof ############################################################################## A very informative answer, dealing with many issues came from prof. Thomas Bally: From: IN%"BALLY%CFRUNI52.BITNET@CEARN.cern.ch" 2-NOV-1994 08:02:49.67 To: IN%"ZUILHOF@CHEM.CHEM.ROCHESTER.EDU" CC: Subj: RHF vs. UHF Dear Mr. Zuilhof, You were asking on CCL about using UHF vs.RHF for calculating the attack of nucleophiles on radical cations. The question of UHF vs. RHF is a thorny one and it becomes thornier when you go to semiempirical methods, even if you disregard for the moment the problems posed by spin contamination which I will address below. By allowing alpha and beta-electrons to occupy different spatial MO's (which is the essence of the UHF model) you take into account a special form of electron correlation called "spin polarization" which expresses itself experimentally in negative hyperfine coupling constants in ESR spectra and is hence a physical phenomenon. However, the UHF model has a tendency to overestimate the extent of spin polarization which results in an overestimation of the stability of systems where spin polarization is important (for example systems containing allylic radical moieties such as they occur quite often in radical ions) if compared to systems where this effect is less important. In semiempirical methods, electron correlation effects are already "absorbed" somehow in the parameters and therefore, in systems with high spin polariza- tion, you count some of these twice in semiempirical UHF calculations. As a consequence, the stability of systems where spin polarization is important (see above) is often *absurdly* overestimated by semiempirical methods. On the other hand, if you do RHF (I suppose you are referring to the "half- electron" method which is used rather than the "real" Roothaan ROHF method in Dewar's modelsbut this makes no difference), you artificially suppress spin polarization entirely (it cannot occur if alpha and bete-electrons are constrained to occupy pairwise the same spatial MO's). Hence the stability of systems where this is important (see above) is *underestimated* with this model. To this you have to add the problem of "high-spin contamination" in UHF wavefunctions which are not eigenfunctions of the S**2 operator and hence cannot be classified as singlets, doublets, triplets. Most decent programs will tell you about the *expectation value* of a UHF wavefunction with regard to S**2 (usually called ) and the deviation of this expectation value from the value for a pure singlet(=0), doublet (=0.75), triplet (=2.75) etc. tells you how far you have gone astray from pure spin states in your calculation. As a rule of thumb, a UHF wavefunction is acceptable if deviates less than 0.1 from the "correct" value. You will find that this deviation is often exceeded, especially in systems with high spin polarization. So what can you do? Unfortunately I cannot give you a good answer. Due to the above-mentioned problems and some other shortcomings of semiempirical methods (problems with small rings) I have personally all but given up semiempirical calculations on radical ions and switched to ab-initio based methods which have become quite affordable with the advent of modern workstations. On the other hand you may get away with semiempirical methods for large systems if (a) You do have cases where spin polarization is unimportant (i.e. if the difference between UHF and RHF heats of formation is, say, less than 5 kcal/mol) (b) If the values for doublets are <0.85. The grist of the matter is, that you should always do *both* RHF and UHF calculations. If the results do not differ substantially, both with regard to geometries and relative energies, you are probably safe (unless you have small rings, but that's another can of worms). Don't hesitate to get back to me if you have follow-up questions or if you need guidance for getting started with ab-initio calculations (of such calculations are feasible for your systems).. thomas bally P.S. please don't reply to the address from where you got this message (I use it exlusively for CCL) but to the one indicated below: ------------------------------------------------------------------------------ | Prof. Thomas Bally | E-mail: Thomas.Bally@unifr.ch | | Institute for Physical Chemistry | | | University of Fribourg | Tel: 011-41-37 826 489 | | Perolles | FAX: 011-41-37 826 488 | | CH-1700 FRIBOURG | | | Switzerland | | ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Both Serge Pachkovsky and John McKelvey commented that MOPAC/AMPAC etc do not implement the REAL/CORRECT ROHF method, but rather Dewar's half-electron method: From: IN%"ps@ocisgi7.unizh.ch" 2-NOV-1994 03:58:29.52 To: IN%"ZUILHOF@CHEM.CHEM.ROCHESTER.EDU" CC: Subj: RE: CCL:ROHF versus UHF in semiempirical calc.'s of radical cations Dear Han, In your message to the CCL you write: > Semiempirical programs such as MOPAC allow the properties of radicals > and radical ions to be calculated with both the Restricted Open-shell > Hartree-Fock method (ROHF) and the Unrestricted Hartree-Fock (UHF) methods. ^^^^ This is not exactly true. Semiempirical programs usually implement half-electron method (and Mopac is not an exception), not ROHF, which is notorious for the poor SCF convergence properties. Although half-electron method often gives results one would expect from the exact ROHF treatment (and in some cases is exactly equivalent to it), there is one important distinction: electronic energy computed within the half-electron approximation is not variational. With my best regards, Serge Pachkovsky. ------------------------------------------------------------------------------ Careful...NONE of the semi-empirical methods derived from MOPAC or AMPAC does the CORRECT ROHF. They all use a half-electron method of Dewar followed by a small C.I. for clean up. Gaussian and GAMESS will do the ROHF for the semiempirical methods correctly, I believe. -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 --------------------------------------------------------------------------- the matter of spin contamination occurring in UHF calculations was adressed by several people: Dave Ewing writes: From: IN%"EWING@jcvaxa.jcu.edu" "DAVID W. EWING (216) 397-4742" To: IN%"ZUILHOF@CHEM.CHEM.ROCHESTER.EDU" CC: Subj: RE: CCL:ROHF versus UHF in semiempirical calc.'s of radical cations With ROHF you don't have to worry about spin contamination. Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu ---------------------------------------------------------------------------- and Irene Newhouse wrote: From: IN%"newhoir@mail.auburn.edu" 3-NOV-1994 12:35:15.41 To: IN%"ZUILHOF@CHEM.CHEM.ROCHESTER.EDU" CC: Subj: RE: CCL:ROHF versus UHF in semiempirical calc.'s of radical cations There are people who are VERY suspicious of ROHF -- people like Andy Holder, one of the authors of AMPAC v4. On the other hand, UHF can, especially very close to the transition state, suffer from 'spin contamination', that is, states with the wrong spin mix in. At very stage, SZ**2 is plotted, so that you can TELL if it's happening. Which way you do it, depends on if you're trying to qualitatively describe experiments, or do a thorough theoretical` investigation. If the former, I'd try it both ways & be happy if the results are about the same. If the latter, all either method is good for is a guess to plug into ab initio computations! Good luck!` Irene Newhouse ############################################################################### ############################################################################### ****************************************************************************** ** Dr. Han Zuilhof ** e-mail: ZUILHOF@chem.chem.rochester.edu ** ** Department of Chemistry ** (optional: ZUILHOF@rulgca.leidenuniv.nl) ** ** University of Rochester ** ** ** Rochester, NY, 14627 ** Fax: (716) 473-6889 ** ** USA ** Voice: (716) 275-2219 ** ****************************************************************************** ** ** ** "Excite a photochemist!" ** ** ** ****************************************************************************** From WANG@IRBM.IT Tue Nov 8 16:24:52 1994 Received: from V1.IRBM.IT for WANG@IRBM.IT by www.ccl.net (8.6.9/930601.1506) id PAA16122; Tue, 8 Nov 1994 15:56:42 -0500 From: Date: Tue, 8 Nov 1994 21:58:11 +0100 (WET) To: chemistry@ccl.net CC: WANG@IRBM.IT Message-Id: <941108215811.68e1@IRBM.IT> Subject: Macromodel_Amber charges Dear all, AMBER force field in Macromodel 4.5 gives guanine (also C, T and U) a net charge of -0.236. Does anyone have the same experience with other molecules ? Thanks, Bingze Wang From PHYSPLMP@MIZZOU1.missouri.edu Tue Nov 8 16:27:49 1994 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.9/930601.1506) id PAA15445; Tue, 8 Nov 1994 15:29:02 -0500 From: Message-Id: <199411082029.PAA15445@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R2) with BSMTP id 1943; Tue, 08 Nov 94 14:24:09 CST Received: by MIZZOU1 (Mailer R2.10 ptf000) id 1662; Tue, 08 Nov 94 14:24:09 CST Date: Tue, 08 Nov 94 14:21:50 CST To: jig@qorg.unizar.es cc: chemistry@ccl.net Subject: Re: CCL:DeFT: Basis sets for Sulfur In-Reply-To: jig@qorg.unizar.es -- Tue, 8 Nov 94 18:21:09 MET I have an interest in sulfur also but have not started DFT calculations yet. I'd appreciate learning any pointers you receive from the net. Thanks in advance. Pat Plummer, Univ. of MO-Columbia From ashy@rose.chem.wesleyan.edu Tue Nov 8 17:26:10 1994 Received: from rose.chem.wesleyan.edu for ashy@rose.chem.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id QAA17007; Tue, 8 Nov 1994 16:35:12 -0500 Received: by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA24432; Tue, 8 Nov 1994 16:29:47 -0500 Date: Tue, 8 Nov 1994 16:29:47 -0500 Message-Id: <9411082129.AA24432@rose.chem.wesleyan.edu> From: Ashwin Dinakar To: chemistry@ccl.net Subject: CCL:Coordinates for Water-Dimer Hello Netters, Iam looking for some references(experimental) on the coordinates for water-dimer. I would appreciate it if your replies are sent directly to me and I will summarize all the responses. Thanks in advance, Ashwin Dinakar, Wesleyan University. From helden@gaucho.ucsb.edu Tue Nov 8 17:31:29 1994 Received: from hub.ucsb.edu for helden@gaucho.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id RAA17487; Tue, 8 Nov 1994 17:11:37 -0500 Received: from gaucho.ucsb.edu by hub.ucsb.edu; id AA06321 sendmail 4.1/UCSB-2.1-sun Tue, 8 Nov 94 14:11:32 PST for chemistry@ccl.net Received: by gaucho.ucsb.edu (AIX 3.2/UCB 5.64/4.03) id AA16903; Tue, 8 Nov 1994 14:10:18 -0800 From: helden@gaucho.ucsb.edu (Gert von Helden) Message-Id: <9411082210.AA16903@gaucho.ucsb.edu> Subject: AMBER parameters for non prot. arginine ? To: chemistry@ccl.net Date: Tue, 8 Nov 1994 14:10:16 +22305458 (PST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1104 Hi everybody We are doing gas phase conformational studies on small protonated peptides. The peptide we started with is Bradykinin. Unfortunately, this peptide has two Argininegroups in it. Since we deal with only singly protonated species, only one arg sidechain is protonated. I looked into amber and there are no parameters for argenine with a non protonated sidechain (which makes sense, since they will be always protonated in solution). So my questions are: a) Did anybody calculated parameters for non protonated arg. b) Are there any standard AMBER atomtypes that could be used for the -C=N-H | NH2 end of the sidechain, so that the only thing to do would be to calulate charges? Thanks for any help, Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From cooksj@ttown.apci.com Tue Nov 8 17:36:21 1994 Received: from ttown.apci.com for cooksj@ttown.apci.com by www.ccl.net (8.6.9/930601.1506) id RAA17453; Tue, 8 Nov 1994 17:08:40 -0500 Received: by ttown.apci.com (5.57/Ultrix3.0-C) id AA21479; Tue, 8 Nov 94 17:11:11 -0500 Date: Tue, 8 Nov 94 17:11:11 -0500 From: cooksj@ttown.apci.com (Stephen J. Cook) Message-Id: <9411082211.AA21479@ttown.apci.com> To: chemistry@ccl.net Subject: Re: CCL:DeFT: Basis sets for Sulfur X-Attribution: sjc Reply-To: cooksj@ttown.apci.com >>>>> "Jose" == Jose Ignacio Garcia writes: Jose> Can anyone to point me to a reference, ftp-site, etc. where find Jose> suitable basis sets for Sulfur to be used in DFT calculations? Jose> Otherwise, how could I to construct the auxiliary basis sets for Jose> this atom? The DGauss basis sets have been made available on the new UniChem web page at http://www.cray.com/apps/UNICHEM/Mainpage.html The basis sets are described in the reference: N. Godbout, D. R. Salahub, J. Andzelm, and E. Wimmer, Can. J. Chem. 70, 560 (1992). -- ********************************************************************* * Steve Cook cooksj@ttown.apci.com * * Air Products and Chemicals, Inc. Tel. (610) 481-2135 * * 7201 Hamilton Blvd. FAX (610) 481-2446 * * Allentown, PA 18195 * * USA * ********************************************************************* * Emacs - the choice of a GNU generation * ********************************************************************* * Disclaimer: The opinions expressed here are those of the author. * * Any resemblance between my opinions and those of Air * * Products is purely coincidental... * ********************************************************************* From steve@carbo.cc.binghamton.edu Tue Nov 8 19:24:54 1994 Received: from carbo.cc.binghamton.edu for steve@carbo.cc.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id TAA19352; Tue, 8 Nov 1994 19:19:59 -0500 Received: by carbo.cc.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA13236; Tue, 8 Nov 94 19:03:58 -0500 Date: Tue, 8 Nov 1994 18:56:21 -0500 (EST) From: Steven Schafer Subject: Q: Molecular Dynamics Animations To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Are there any public domain programs for Silicon Graphics systems that can take a dynamics run from SYBYL and create a movie from it? Also, what visualization programs support input from GAMESS? Thanks in advance, Steven Schafer S.U.N.Y. Binghamton Chemistry Department Binghamton, New York From ungsik@radon.sait.samsung.co.kr Tue Nov 8 19:29:59 1994 Received: from han.hana.nm.kr for ungsik@radon.sait.samsung.co.kr by www.ccl.net (8.6.9/930601.1506) id TAA19279; Tue, 8 Nov 1994 19:14:44 -0500 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA04092; Wed, 9 Nov 94 09:07:04 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA29294; Wed, 9 Nov 94 09:15:08 KST Received: by radon.sait.samsung.co.kr (931110.SGI/920502.SGI) for @saitgw.sait.samsung.co.kr:CHEMISTRY@ccl.net id AA03296; Wed, 9 Nov 94 09:14:09 +0900 Date: Wed, 9 Nov 94 09:14:09 +0900 From: ungsik@radon.sait.samsung.co.kr (Ungsik Yu) Message-Id: <9411090014.AA03296@radon.sait.samsung.co.kr> To: CHEMISTRY@ccl.net Subject: metallocene parameters Hi, Does anyone have force field parameters for the Ti and Zr atmos which will be used for the modeling of metallocene catalysts? Also does anyone have geometric parameters for the common metallocene catalysts such as cyclopentadienyl or indenyl zirconium dichloride? I plan to use Biosym/DISCOVER for classical calculations and Cray/UNICHEM (DGauss and MNDO 93) and Gaussian 92 for quantum chemical calculations. Any help is appreciated. Thanks, Ungsik ---------------------------------------------------------------- Ungsik Yu, Ph.D. ungsik@radon.sait.samsung.co.kr Samsung Adv. Inst. Tech. P.O. Box 111, Suwon, 440-600, KOREA Tel: 82-331-280-9169 Fax: 82-331-280-9158 ----------------------------------------------------------------