From h.rzepa@ic.ac.uk Fri Oct 28 05:21:48 1994 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA16255; Fri, 28 Oct 1994 05:05:14 -0400 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Fri, 28 Oct 1994 09:05:00 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA20806; Fri, 28 Oct 94 09:04:54 GMT X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Oct 1994 10:05:00 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) Subject: PDB reader for Mac will be RasMac Cc: Sayle Dr R A >> Dear netters, >> >> I would like to know what are the names of some of the molecular >> modelling programs for a Mac to read pdb files. I recalled seeing some, >> but have since forgotten the name. I would help if it was a public >> domain program too. I am trying to make slides for an organic chemist for >> his protein structure class. >> >> Thank you very much in advance. >> >> Nicholas Lee >> glee@chem0sun.calstatela.edu You may wish to know that a version of Ramol called RasMac is currently in bet test, and should be available for pdb processing soon. Also the Richardson's Kinemage package can read and then display protein files. Both are/will be free as far as I am aware, and need no license at all. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.03, 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 winn@tph12.tuwien.ac.at Fri Oct 28 07:21:38 1994 Received: from tph12.tuwien.ac.at for winn@tph12.tuwien.ac.at by www.ccl.net (8.6.9/930601.1506) id GAA17155; Fri, 28 Oct 1994 06:28:03 -0400 Message-Id: <199410281028.GAA17155@www.ccl.net> Received: by tph12.tuwien.ac.at (1.37.109.4/16.2) id AA16039; Fri, 28 Oct 94 11:30:43 +0100 From: Martyn Winn Subject: 100% parallel MD To: chemistry@ccl.net Date: Fri, 28 Oct 94 11:30:43 MEZ Mailer: Elm [revision: 70.85] Teerakiat, My feeling is that your scheme should work, provided you also reverse quantities such as the 3rd derivative of the positions (needed in a predictor-corrector algorithm). It should then be entirely equivalent to running the simulation backwards in time. With regard to Song Ling's objection, he is right that the two trajectories do not connect in phase space after the transformation p -> -p (to take his harmonic oscillator example). However, my understanding is that you would make the transformation -p -> p after the run, thus reconnecting the trajectories. Martyn -- ***************** Dr. Martyn Winn ************************************** \ / \ Institut fuer Theoretische Physik, Technische Universitaet Wien, / \ Wiedner Hauptstrasse 8-10, A-1040 Wien, Austria. / \____ ____________/ \ Tel: +43 1 58801 5678 / \ Fax: +43 1 5867760 / \ E-mail: winn@tph12.tuwien.ac.at / \ / -------------------------------------- From ARILAHTI@finabo.abo.fi Fri Oct 28 08:21:43 1994 Received: from SILKE.ABO.FI for ARILAHTI@finabo.abo.fi by www.ccl.net (8.6.9/930601.1506) id HAA18129; Fri, 28 Oct 1994 07:57:04 -0400 From: Received: from finabo.abo.fi by finabo.abo.fi (PMDF V4.3-8 #7828) id <01HIT8B1R580BYTG5W@finabo.abo.fi>; Fri, 28 Oct 1994 13:56:53 EET Date: Fri, 28 Oct 1994 13:56:53 +0200 (EET) Subject: MOPAC necessarily batch? To: chemistry@ccl.net Message-id: <01HIT8B1SHG2BYTG5W@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 I need to start a lot (>100) of MOPAC runs one after another from a UNIX script. How can I make sure that no more than one MOPAC is running at a time? I have tried deleting '&' from the .com file, but MOPAC still goes batch (obviously the routine 'ta_batch' makes it do so in any case). I have tried adding 'wait' in my script, but - strangely enough - it doesn't seem to work either. 'at' would be clumsy to be used in my case. So, how could I either make MOPAC run in the foreground or make my script wait for the batch to end? Thanks in advance. Ari Lahti, Abo Akademi University -------------------------------------------------------------- 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 fdeprof@is1.vub.ac.be Fri Oct 28 09:21:39 1994 Received: from rc1 for fdeprof@is1.vub.ac.be by www.ccl.net (8.6.9/930601.1506) id JAA19932; Fri, 28 Oct 1994 09:19:30 -0400 Received: from is1e.vub.ac.be by rc1 (8.6.8.1/2.24.ap) id OAA13680; Fri, 28 Oct 1994 14:19:59 +0100 Received: from sterfpmc215.vub.ac.be by is1e.vub.ac.be (5.61/BFUCC-920211) id AA20174; Fri, 28 Oct 94 14:17:40 +0100 Date: Fri, 28 Oct 94 14:17:40 +0100 Message-Id: <9410281317.AA20174@is1e.vub.ac.be> X-Sender: fdeprof@is1.vub.ac.be (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: fdeprof@is1.vub.ac.be Subject: Sodalite cage Hi all, I'm looking for coordinates of the sodalite cage and (if possible) other structural units in zeolite type systems for the use in quantum chemical calculations. Is there anyone who could share this information with me ? I will summarize for the net. Frank De Proft Eenheid Algemene Chemie Vrije Universiteit Brussel From janrad@tiger.chem.uw.edu.pl Fri Oct 28 09:24:26 1994 Received: from tiger.chem.uw.edu.pl for janrad@tiger.chem.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id IAA19346; Fri, 28 Oct 1994 08:50:15 -0400 Received: by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA12981; Fri, 28 Oct 1994 13:50:05 +0200 Date: Fri, 28 Oct 1994 13:50:05 +0200 From: janrad@tiger.chem.uw.edu.pl (Jan Radomski) Message-Id: <9410281150.AA12981@tiger.chem.uw.edu.pl> To: chemistry@ccl.net Subject: computer accessibe databases Cc: janrad@tiger.chem.uw.edu.pl ---- Dear Netters, I am interested in contact with anyone willing to share their experience on acquiring, installing, running, etc. any kind of spectral, structural, QSAR, safety or any other chemical and material sciences computer database. Public domain, shareware as well as commercial. Of special interest are ease of use, availability of internal data formats, ASCII exports, portability, and of course cost. Please e-mail me direct, I'll summarize for the net if there would be suf- ficient interest. Jan Radomski From bryan@chem.columbia.edu Fri Oct 28 11:22:14 1994 Received: from cucbs.chem.columbia.edu for bryan@chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id KAA21598; Fri, 28 Oct 1994 10:38:12 -0400 Received: by cucbs.chem.columbia.edu id AA19215 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 28 Oct 1994 10:42:19 -0400 Date: Fri, 28 Oct 1994 10:42:19 -0400 From: netraM nayrB Message-Id: <199410281442.AA19215@cucbs.chem.columbia.edu> To: chemistry@ccl.net Subject: CACAO help Is there a list server for CACAO? Or other forums for getting help in running the program? In particular, for a friend who is an experimental organic chemist who is having trouble with the input files? Informative emailed responses will be posted later. Thanks, bryan@chem.columbia.edu From tudor@t10.Lanl.GOV Fri Oct 28 13:21:49 1994 Received: from transposon.lanl.gov for tudor@t10.Lanl.GOV by www.ccl.net (8.6.9/930601.1506) id MAA24968; Fri, 28 Oct 1994 12:45:43 -0400 Received: from temin.lanl.gov by transposon.lanl.gov (4.1/SMI-4.1) id AA14512; Fri, 28 Oct 94 10:45:38 MDT Date: Fri, 28 Oct 94 10:45:38 MDT From: tudor@t10.Lanl.GOV (Tudor Oprea) Message-Id: <9410281645.AA14512@transposon.lanl.gov> To: chemistry@ccl.net Subject: Running Mopac in batch from SYBYL This was posted yesterday. I assume the SPL may be useful to others.. >> From: arilahti@abo.fi < Ari Lahti > >> Date: Fri, 28 Oct 1994 13:56:53 +0200 (EET) >> Subject: CCL:MOPAC necessarily batch? >> >> I need to start a lot (>100) of MOPAC runs one after another >> from a UNIX script. How can I make sure that no more than one >> MOPAC is running at a time? >> >> I have tried deleting '&' from the .com file, but MOPAC still >> goes batch (obviously the routine 'ta_batch' makes it do so in >> any case). I have tried adding 'wait' in my script, but - >> strangely enough - it doesn't seem to work either. 'at' would >> be clumsy to be used in my case. >> >> So, how could I either make MOPAC run in the foreground or >> make my script wait for the batch to end? >> >> >> Thanks in advance. >> >> Ari Lahti, Abo Akademi University >> >> >> -------------------------------------------------------------- >> >> 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 >> >> --------------------------------------------------------------- Ari, From the 'ta_batch' keyword I assume that you wish to run these in Sybyl. There are several ways to do this: one is to get a stand alone verision of Mopac from QCPE and have it run from a shell script (like the one written by Manish Sud from Biosym), and that will run Mopac in batch. This would help UPGRADE your Mopac from 5.0 to Mopac93, by the way.. another way is to tell Sybyl to use the 'at' command - which you can find using menubar to run Mopac - it will prompt you to 'run_it_now' and you can put each job to start after 30 min or 1 hr (whatever your estimate for 1 job is). Another way, to run it interactively in SYBYL, is to introduce the following SPL into Sybyl (with the take command) and have both Sybyl and Mopac run - essentially the script awaits for the *.sta file to be written (which is done when Mopac has successfully run in the Sybyl version), and then launch the next one. The script was written by me and Chris L. Waller .. and for a while i found it useful.. ## This is to run Mopac AM1 via MOPAC 5 in Sybyl for ALL molecules in database ## Written by Tudor I. Oprea and Chris L. Waller ## First tell Sybyl it's a macro called am1 uims define macro am1 sybylbasic ## Then stop the [C],[G] or [Q] set cgq 0 ## input database name setvar a %prompt(string "database" "Enter database name") ## open database in read_only mode da op $a re ## Start reading molecules in for processing for i in %database(*) da get "$i" m1 ## Look for mopac DONE jobs if %not(%dir($i.sta)) echo calculating MOPAC AM1 ... ## NOTE: CHANGE TO SUIT - USE geo_all OR 1SCF for geometry ## and method (AM1, PM3 etc.) to change Hamiltonian qcpe m1 mopac setup $i \ method am1 \ time 6200 \ other "NOINTER GRAPH" \ ## NOTE: For Sulfur you need a file called PAR for the ## S parameters, and the EXTERNAL=PAR PARASOK keywords above!!! done \ "$i" 'machine_NAME' run_it_now ## change 'machine_NAME' to suit ## Now wait for this calculation to finish before starting a new one while %not(%dir($i.sta)) echo process MOPAC still RUNNING echo to keep the succession, do not press C,G or Q now! wait 60 endwhile echo mopac DONE ## If this molecule was already calculated, skip the whole procedure else echo this molecule is already Mopac DONE! endif endfor . ## NOTE: do not delete the '.' after endfor - it's needed in SYBYL --Tudor **************************************************************************** * Tudor I. Oprea, MD PhD Tel: (505) 667 2682 * * Postdoctoral Research Associate Fax: (505) 665 3493 * * Theoretical Biology and Biophysics (T-10) Email: * * Los Alamos National Laboratory tudor@t10.lanl.gov * * Mail Stop K710, Los Alamos NM 87545 * **************************************************************************** From sling@euclid.chem.washington.edu Fri Oct 28 14:21:53 1994 Received: from euclid.chem.washington.edu for sling@euclid.chem.washington.edu by www.ccl.net (8.6.9/930601.1506) id NAA25870; Fri, 28 Oct 1994 13:25:20 -0400 Received: by euclid.chem.washington.edu (AIX 3.2/UCB 5.64/4.03) id AA32889; Fri, 28 Oct 1994 10:24:33 -0700 Date: Fri, 28 Oct 1994 10:24:33 -0700 From: sling@euclid.chem.washington.edu (Song Ling) Message-Id: <9410281724.AA32889@euclid.chem.washington.edu> To: chemistry@ccl.net, winn@tph12.tuwien.ac.at Subject: Re: CCL:100% parallel MD Cc: sling@euclid.chem.washington.edu Dr. Winn's reconnection scheme is definitely correct, and in principle it is equivalent to integrating backward as I suggested earlier. One needs the 3rd derivatives because predictor-corrector is not self-starting (unless one uses Runge-Kutta which is slow). Two questions remain, one is computational: Will the -dt, dt approach be more efficient than the "conventional" 2dt forward method? The other is "fundamental": Will the -dt, dt approach generate the "same" trajectory as the 2dt one if the system is sensitive to initial conditions? I'd like to learn about the answers. From tudor@t10.Lanl.GOV Fri Oct 28 14:24:37 1994 Received: from transposon.lanl.gov for tudor@t10.Lanl.GOV by www.ccl.net (8.6.9/930601.1506) id OAA26605; Fri, 28 Oct 1994 14:06:41 -0400 Received: from temin.lanl.gov by transposon.lanl.gov (4.1/SMI-4.1) id AA14798; Fri, 28 Oct 94 12:06:40 MDT Date: Fri, 28 Oct 94 12:06:40 MDT From: tudor@t10.Lanl.GOV (Tudor Oprea) Message-Id: <9410281806.AA14798@transposon.lanl.gov> To: chemistry@ccl.net Subject: Running Mopac in SYBYL - the SEQUEL Folks, my E-mail system interprets a single dot '.' on a line as the 'EOT' (or Ctrl-D) signal. Thus, the previous message is INCOMPLETE. Any SYBYL MACRO needs to end with a '.' on a single line. So here is the completion of the message.. I assume the interested parties can cut and paste into the previous one. endfor . ## NOTE: do not delete the '.' after endfor - it's needed in SYBYL **************************************************************************** * Tudor I. Oprea, MD PhD Tel: (505) 667 2682 * * Postdoctoral Research Associate Fax: (505) 665 3493 * * Theoretical Biology and Biophysics (T-10) Email: * * Los Alamos National Laboratory tudor@t10.lanl.gov * * Mail Stop K710, Los Alamos NM 87545 * **************************************************************************** From glee@chem0sun.calstatela.edu Fri Oct 28 15:21:45 1994 Received: from eagle.calstatela.edu for glee@chem0sun.calstatela.edu by www.ccl.net (8.6.9/930601.1506) id OAA28272; Fri, 28 Oct 1994 14:51:54 -0400 Received: from neptune.calstatela.edu by eagle.calstatela.edu with SMTP id AA17858 (5.65c/IDA-1.4.4 for ); Fri, 28 Oct 1994 11:50:49 -0700 Received: from chem0sun.calstatela.edu by neptune.calstatela.edu (4.1/SMI-4.1) id AA18966; Fri, 28 Oct 94 11:48:35 PDT Received: by chem0sun.calstatela.edu (4.1/SMI-4.1) id AA02263; Fri, 28 Oct 94 11:47:20 PDT Date: Fri, 28 Oct 94 11:47:20 PDT From: glee@chem0sun.calstatela.edu (Ging Lee 12-06-90) Message-Id: <9410281847.AA02263@chem0sun.calstatela.edu> To: chemistry@ccl.net Subject: sequential execution of Mopac Dear Ari Lahti, Abo Akademi University, I have run mopac job in sequence before and the way I did it was to creat a file that contains the entire list of input file without its extension (.dat). I would called the file "list"; the script file to run it would be called "runlist". The content of "runlist" is: files=`cat list` for file in $files do /net/sgi1/exec/mopac6/bin/Mopac.e $file ----------------------------------------------------------------- (change your path to locate the executable file for mopac; this also assumes that your mopac program will give the appropriate output extensions. The file "runlist" should have executable permission by: % chmod u+x runlist To run your job in the background just type % runlist & Hope this helps, if you have any question email me. Nicholas Lee glee@chem0sun.calstatela.edu From garciae@ucsub.Colorado.EDU Fri Oct 28 19:21:44 1994 Received: from ucsub.Colorado.EDU for garciae@ucsub.Colorado.EDU by www.ccl.net (8.6.9/930601.1506) id TAA01840; Fri, 28 Oct 1994 19:02:31 -0400 Received: (from garciae@localhost) by ucsub.Colorado.EDU (8.6.9/8.6.9/CNS-3.5) id RAA04500; Fri, 28 Oct 1994 17:02:00 -0600 Date: Fri, 28 Oct 1994 17:01:45 -0600 (MDT) From: Garcia Edgardo To: CHEMISTRY@ccl.net Subject: CLL: Mac PDB reader Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For reading PDB files with the Mac you can use : 1. Alchemy III 2. CSC Chem 3D Plus 3.1 (not expensive) The second program can read/write in many different formats is very easy to use, you can use it to translate your files formats for use with your best molecular ploting program ! You can contact CSC people at: support@camsci.com 617-491-6862 (phone) 617-491-8208 (fax) Edgardo Garcia Cristol Chem & Biochem Univ. of Colorado, Boulder CO, USA From grechtst@pepvax.pepperdine.edu Fri Oct 28 21:21:47 1994 Received: from pepvax.pepperdine.edu for grechtst@pepvax.pepperdine.edu by www.ccl.net (8.6.9/930601.1506) id UAA02610; Fri, 28 Oct 1994 20:31:58 -0400 Received: by pepvax.pepperdine.edu (5.65c/IDA-1.4.4/Pep-5.1) id AA02218 for chemistry@ccl.net; Fri, 28 Oct 1994 17:32:19 -0700 From: Gregory Rechtsteiner Message-Id: <199410290032.AA02218@pepvax.pepperdine.edu> Subject: Porphyrin Files? To: chemistry@ccl.net Date: Fri, 28 Oct 94 17:32:19 PDT X-Mailer: ELM [version 2.3 PL11] Hello: I am doing a presentation (soon) and I wanted to use a nice, high quality picture of a porphrin (witn no specific metal in the center). I was wondering if any of the subscribers of this list could help me out. Thank you for your time and bandwidth, Gregory -- -------------------------------------------------------------------------------- Gregory A. Rechtsteiner Pepperdine University Research Assistant 24255 PCH # 572 Fax: 310.456.4314 (work) Malibu, CA. 90263 grechtst@pepvax.pepperdine.edu / grechtst@netcom.com --------------------------------------------------------------------------------