From chemistry-request@server.ccl.net Wed Sep 18 03:30:10 2002 Received: from ns9.mmaweb.net ([64.71.143.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8I7UAw09591 for ; Wed, 18 Sep 2002 03:30:10 -0400 Received: from chemaxon.com (user254.obuda.axelero.hu [195.228.88.254]) by ns9.mmaweb.net (8.11.0/8.11.0) with ESMTP id g8I7TH011806; Wed, 18 Sep 2002 03:29:17 -0400 (EDT) Message-ID: <3D882B5A.8040507@chemaxon.com> Date: Wed, 18 Sep 2002 09:29:30 +0200 From: Ferenc Csizmadia Organization: ChemAxon User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, hu, zh MIME-Version: 1.0 To: chemweb@ic.ac.uk, CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, scitech@lists.apple.com Subject: New releases of Marvin, JChem, JKlustor - software for the manipulation of chemical structures Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Apologies for multiple postings. Marvin Applets and Marvin Beans 2.10.5, JChem and JKlustor 1.7.3 have been released. The packages contain Java software development tools and applications for chemistry. The software is portable (runs in Windows, Mac, Unix, etc.) - Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. - JChem provides chemical database searching capabilities by integration into relational database engines supporting SQL. - JKlustor is a software for diversity calculations and clustering, which can generate and apply 2D molecular fingerprints. FREE: - Marvin Applets are free for free web sites. - MarvinSketch and MarvinView applications accessed from ChemAxon's web site http://www.chemaxon.com/marvin/jnlp/index.html - Locally installed MarvinSketch, MarvinView, and MolConverter applications are free for academic or home users. Marvin News: - Improved Mac support http://www.chemaxon.com/marvin/doc/for-mac-users.html - Signed applets (File Open, Save, and copy/paste support) http://www.chemaxon.com/marvin/doc/signing.html - Full featured MarvinSketch and MarvinView applications can be accessed directly from the web without installation (applying the Java Web Start technology) http://www.chemaxon.com/marvin/jnlp/index.html - CML import http://www.chemaxon.com/marvin/doc/formats.html - Scalable Vector Graphics (SVG) image file generation http://www.chemaxon.com/marvin/doc/images-doc.html - Atom mapping http://www.chemaxon.com/marvin/doc/example-sketch3.5.html - Copy/paste with ChemDraw http://www.chemaxon.com/marvin/doc/datatransfer.html - See more at http://www.chemaxon.com/marvin/doc/changes.html http://www.chemaxon.com/marvin JChem News: - DB2 and PostgreSQL support added - Search using R-group conditions (Markush structures) - New query atom conditions (aliphatic/aromatic, valence, connection count, hydrogen connection count, ring count, smallest ring size) - Detailed guide for structure searching http://www.jchem.com/doc/user/ - See more at http://www.jchem.com/changes.html http://www.jchem.com JKlustor News: - JChem API includes JKlustor http://www.jchem.com/doc/api/ - See more at http://www.jchem.com/changes.html http://www.jchem.com/doc/admin/JKlustor.html The software can be tried/downloaded at http://www.chemaxon.com/products.html Online demos: http://www.chemaxon.com/marvin/demos.html http://www.jchem.com/examples.html Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon http://www.chemaxon.com From chemistry-request@server.ccl.net Wed Sep 18 05:33:38 2002 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8I9Xbw12847 for ; Wed, 18 Sep 2002 05:33:38 -0400 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id g8I9i2g16483 for ; Wed, 18 Sep 2002 17:44:02 +0800 Date: Wed, 18 Sep 2002 17:44:02 +0800 (HKT) From: Ng Man Fai To: CHEMISTRY@ccl.net Subject: Onsager equation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, may I ask that how to implement the Onsager equation for calculating the solvent effect in the excited state calculations? I have changed the ground state fock matrix by adding the dielectric term, but where to put the index of refraction term? Best regards, Andy From chemistry-request@server.ccl.net Mon Sep 16 11:41:52 2002 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8GFfqw07940 for ; Mon, 16 Sep 2002 11:41:52 -0400 Received: from 10.1.0.50 by srvus010.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 16 Sep 2002 11:41:19 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0H2J00D2KFAO4G@lvlmail.unitedcatalysts.com>; Mon, 16 Sep 2002 11:35:12 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Mon, 16 Sep 2002 11:38:07 -0400 Content-return: allowed Date: Mon, 16 Sep 2002 11:38:07 -0400 From: "Shobe, Dave" Subject: RE: activation energy To: "'Jolanta Latosinska'" Cc: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C1604B@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g8GFfqw07941 Activation energy for what reaction? If you mean the inversion of the nitrogen lone pair, I imagine that would be difficult to measure experimentally with tunnelling and with rotation of the group. Inversion activation energies for tertiary amines have been measured, though, as they are far less problematic. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Jolanta Latosinska [mailto:jolanala@amu.edu.pl] Sent: Saturday, September 14, 2002 8:53 AM To: chemistry@ccl.net Subject: CCL:activation energy Dear Netters, I am looking for the experimental value of the activation energy of the typical NH2 group. Could you help me please? Kind regards, Jolanta -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Sep 17 16:59:21 2002 Received: from cobalt.cem.uct.ac.za ([137.158.164.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HKxHw22348 for ; Tue, 17 Sep 2002 16:59:18 -0400 Received: from localhost (csimpson@localhost) by cobalt.cem.uct.ac.za (8.11.2/8.11.2) with ESMTP id g8HL7HC28899 for ; Tue, 17 Sep 2002 23:07:20 +0200 X-Authentication-Warning: cobalt.cem.uct.ac.za: csimpson owned process doing -bs Date: Tue, 17 Sep 2002 23:07:16 +0200 (SAST) From: Chas Simpson X-X-Sender: To: "chemistry@ccl.net" Subject: localization schemes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I've seen in the Gaussian programmers manual that the Boys Localization scheme is available with the Boyloc routine however I'm a bit stumped how to actually use it. Secondly, it doesn't appear that there is any other localization scheme available in G98. Are there any freely available programs that implement the Edmiston-Ruedenberg, von Niessen or Pipek-Mezey schemes? I think some of these are implemented in GAMESS.....??? Thanks for your help. I will summarize. Chas _______________________________________________ Chas Simpson Computational Chemistry University of Cape Town South Africa e-mail: csimpson@hydrogen.cem.uct.ac.za http://hydrogen.cem.uct.ac.za/compchem/ _______________________________________________ From chemistry-request@server.ccl.net Mon Sep 16 17:07:09 2002 Received: from hotmail.com ([64.4.14.184]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GL78w12907 for ; Mon, 16 Sep 2002 17:07:08 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 16 Sep 2002 14:07:03 -0700 Received: from 68.47.203.89 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 16 Sep 2002 21:07:03 GMT X-Originating-IP: [68.47.203.89] From: "Matt Ericson" To: chemistry@ccl.net Subject: Looking for cc-pcvqz basis set for Cl Date: Mon, 16 Sep 2002 17:07:03 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 16 Sep 2002 21:07:03.0578 (UTC) FILETIME=[018D67A0:01C25DC5] I am looking for a correlation-consistent core-valence basis set for Cl, preferably cc-pcvqz or aug-cc-pcvqz. I was unable to find one at the EMSL basis set library or in several Google searches. If any of you have that basis set, or a link/reference to a paper where it was published, I would appreciate it if you could email me the information at mattericson@hotmail.com. Thank you. _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From chemistry-request@server.ccl.net Mon Sep 16 21:43:32 2002 Received: from web12801.mail.yahoo.com ([216.136.174.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8H1hWw28958 for ; Mon, 16 Sep 2002 21:43:32 -0400 Message-ID: <20020917014331.75841.qmail@web12801.mail.yahoo.com> Received: from [203.87.150.242] by web12801.mail.yahoo.com via HTTP; Mon, 16 Sep 2002 18:43:31 PDT Date: Mon, 16 Sep 2002 18:43:31 -0700 (PDT) From: amor san juan Subject: Re: CCL:autodock To: Venkataraman Kabaleeswaran Cc: chemistry@ccl.net In-Reply-To: <200209162247.g8GMlD504373@medusa.wo.utoledo.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I suggest you use AutoDock Tools (ADT) downloadable at autodock site. Cheers, Amor --- Venkataraman Kabaleeswaran wrote: > I am new user to autodock. I have difficulities in > converting from pdb to > mol2 ...to pdbqs. Finally I made those with long > way, assumeing there > is some easy way to do that. > > I have problem in making grid parameter file , while > doing mkgpf3 lig.pdbq > macro.pdbqs I got an error message " autogrid is too > large"etc > > Is there any easy way or script to convert the pdb > files to autodock pbq or > pdbqs etc......and also step by step way to dock the > ligand by user friendly. > > > thanks in advance > venkataraman > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From chemistry-request@server.ccl.net Tue Sep 17 11:03:38 2002 Received: from neon.ch.pwr.wroc.pl ([156.17.3.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HF3bw15836 for ; Tue, 17 Sep 2002 11:03:38 -0400 Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (SGI-8.9.3/8.9.3) with ESMTP id QAA52407 for ; Tue, 17 Sep 2002 16:58:14 -0700 (PDT) Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <3D87C195.7D0A2C0@neon.ch.pwr.wroc.pl> Date: Tue, 17 Sep 2002 16:58:14 -0700 From: Jolanta Grembecka X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: distance matrix problem Content-Type: multipart/alternative; boundary="------------6B41264AD05EF3EEA6328AF9" --------------6B41264AD05EF3EEA6328AF9 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: base64 Dear CCLers, I have a problem with the distance matrix during the optimization (gaussian98) of the system, part of which is froozen during the calculations. This is a part of the enzyme active site and the inhibitor. The end of the output is as follow: D334 3.00088 0.00024 0.00272 0.00000nan nan D335 0.92993 0.00005 0.00290 0.00000nan nan D336 2.83744 0.00010 -0.00358 0.00000nan nan D337 -0.45183 -0.00004 0.00344 0.00000nan nan D338 -1.32264 -0.00013 -0.00367 0.00000nan nan D339 1.67128 -0.00028 0.00334 0.00000nan nan D340 0.74944 0.00011 -0.00367 0.00000nan nan D341 -2.53983 -0.00005 0.00335 0.00000nan nan D342 -0.27057 -0.00035 0.00579 0.00000nan nan D343 2.87577 -0.00027 0.00477 0.00000nan nan D344 3.01943 -0.00020 -0.00125 0.00000nan nan D345 -0.11741 -0.00008 -0.00227 0.00000nan nan D346 3.12886 -0.00006 -0.00954 0.00000nan nan D347 -0.23854 -0.00024 -0.00380 0.00000nan nan D348 -0.01760 -0.00017 -0.00850 0.00000nan nan D349 2.89818 -0.00035 -0.00276 0.00000nan nan D350 3.05693 0.00040 -0.01212 0.00000nan nan D351 -0.07232 0.00009 -0.00666 0.00000nan nan D352 -0.07999 0.00049 -0.01312 0.00000nan nan D353 3.07395 -0.00026 -0.00767 0.00000nan nan D354 -1.48761 0.00004 -0.01471 0.00000nan nan D355 0.96205 -0.00035 0.01705 0.00000nan nan D356 1.64210 0.00005 -0.01996 0.00000nan nan D357 -2.19142 -0.00007 0.01180 0.00000nan nan Item Value Threshold Converged? Maximum Force 0.002762 0.000450 NO RMS Force 0.000281 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement nan 0.001200 YES Predicted change in Energy=nan GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Problem with the distance matrix. Error termination via Lnk1e in /usr/local/appl_g98_A9/g98/l202.exe. Job cpu time: 10 days 21 hours 55 minutes 14.4 seconds. File lengths (MBytes): RWF= 306 Int= 0 D2E= 0 Chk= 40 Scr= 1 ------- Does anybody know what is the reason and how to solve the problem? Best regards, Jolanta Grembecka -- ************************************ * Jolanta Grembecka PhD * * Institute of Organic Chemistry * * Biochemistry and Biotechnology * * Wroclaw University of Technology * * 50-370 Wroclaw * * Wybrzeze Wyspianskiego 27 * * POLAND * * tel. +48+713202137 * * http://tytan.bf.uni.wroc.pl/jola * ************************************ --------------6B41264AD05EF3EEA6328AF9 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,
I have a problem with the distance matrix during the optimization (gaussian98) of the system, part of which is froozen during the calculations. This is a part of the enzyme active site and the inhibitor. The end of the output is as follow:
 

   D334       3.00088   0.00024   0.00272   0.00000nan       nan
   D335       0.92993   0.00005   0.00290   0.00000nan       nan
   D336       2.83744   0.00010  -0.00358   0.00000nan       nan
   D337      -0.45183  -0.00004   0.00344   0.00000nan       nan
   D338      -1.32264  -0.00013  -0.00367   0.00000nan       nan
   D339       1.67128  -0.00028   0.00334   0.00000nan       nan
   D340       0.74944   0.00011  -0.00367   0.00000nan       nan
   D341      -2.53983  -0.00005   0.00335   0.00000nan       nan
   D342      -0.27057  -0.00035   0.00579   0.00000nan       nan
   D343       2.87577  -0.00027   0.00477   0.00000nan       nan
   D344       3.01943  -0.00020  -0.00125   0.00000nan       nan
   D345      -0.11741  -0.00008  -0.00227   0.00000nan       nan
   D346       3.12886  -0.00006  -0.00954   0.00000nan       nan
   D347      -0.23854  -0.00024  -0.00380   0.00000nan       nan
   D348      -0.01760  -0.00017  -0.00850   0.00000nan       nan
   D349       2.89818  -0.00035  -0.00276   0.00000nan       nan
   D350       3.05693   0.00040  -0.01212   0.00000nan       nan
   D351      -0.07232   0.00009  -0.00666   0.00000nan       nan
   D352      -0.07999   0.00049  -0.01312   0.00000nan       nan
   D353       3.07395  -0.00026  -0.00767   0.00000nan       nan
   D354      -1.48761   0.00004  -0.01471   0.00000nan       nan
   D355       0.96205  -0.00035   0.01705   0.00000nan       nan
   D356       1.64210   0.00005  -0.01996   0.00000nan       nan
   D357      -2.19142  -0.00007   0.01180   0.00000nan       nan
         Item               Value     Threshold  Converged?
 Maximum Force            0.002762     0.000450     NO
 RMS     Force            0.000281     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     nan          0.001200     YES
 Predicted change in Energy=nan
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

 Problem with the distance matrix.
 Error termination via Lnk1e in /usr/local/appl_g98_A9/g98/l202.exe.
 Job cpu time: 10 days 21 hours 55 minutes 14.4 seconds.
 File lengths (MBytes):  RWF=  306 Int=    0 D2E=    0 Chk=   40 Scr=    1
-------

Does anybody know what is the reason and how to solve the problem?
Best regards,
Jolanta Grembecka
  

-- 
************************************
* Jolanta Grembecka PhD            *
* Institute of Organic Chemistry   *
* Biochemistry and Biotechnology   *
* Wroclaw University of Technology *
* 50-370 Wroclaw                   *
* Wybrzeze Wyspianskiego 27        *
* POLAND                           *
* tel. +48+713202137               * 
* http://tytan.bf.uni.wroc.pl/jola *
************************************
  --------------6B41264AD05EF3EEA6328AF9-- From chemistry-request@server.ccl.net Wed Sep 18 13:16:44 2002 Received: from laplinux.ethz.ch ([129.132.118.154]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IHGiw23901 for ; Wed, 18 Sep 2002 13:16:44 -0400 Received: from laplinux.ethz.ch (localhost [127.0.0.1]) by laplinux.ethz.ch (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g8IHGmYE004140; Wed, 18 Sep 2002 19:16:48 +0200 Received: from localhost (acontini@localhost) by laplinux.ethz.ch (8.12.3/8.12.3/Submit) with ESMTP id g8IHGlIN004137; Wed, 18 Sep 2002 19:16:47 +0200 X-Authentication-Warning: laplinux.ethz.ch: acontini owned process doing -bs Date: Wed, 18 Sep 2002 19:16:47 +0200 (CEST) From: Alessandro Contini X-X-Sender: acontini@laplinux.ethz.ch To: Dario Narducci cc: chemistry@ccl.net Subject: Re: CCL:frequency calculations using MP2 in Gaussian In-Reply-To: <5.1.0.14.0.20020917143614.02483730@titanium.mater.unimib.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g8IHGiw23902 Hi Dario, the problem is that your Hard Disk is not so big as you think; the scratck files for an MP2 calculation could easyly reach and pass the 2GB; the other problem is the ammount of ram, that could not be enough for a direct calculation in MP2 (not enough for having results in a reasonable time on a medium size sistem with a 6-31G+(d) basis), but the best thing to do is trying anyway a direct SCF calculation (keyword SCF(direct)). Best reguards Alessandro Dott. Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Tue, 17 Sep 2002, Dario Narducci wrote: > Hello to everybody, > > I'm using Gaussian98 (Linux, 64 MB RAM, more than 2 GB of avail. HD). > Trying to compute vibrational spectra using RHF/MP2 (direct) I get the > following error message : > "Erroneous write during file extend. write 237567 instead of 4096 Probably > out of disk space" after which the job dies. > > My input file is: > %nproc=2 > %mem=15MW > #p MP2/6-31G** FREQ=NoRaman > > When trying to use instead MP2(Fulldirect) the message changes into "Cannot > use MP2=Incore or MP2=FullDirect for this calculation." > > As, when I use this option for an optimization run, it works well, I wonder > how I could menage to compute vibrational frequencies with MP2. > > Any suggestion welcome. Thanks > > > > > > ================================= oOo ============================== > Prof. Dario Narducci, Univ. of Milano Bicocca > Dept. of Materials Science, v. R. Cozzi 53, I-20125 Milano > ph. +39-02-6448-5137, fax -5400, mailto:dario.narducci@unimib.it > http://www2.mater.unimib.it/narducci/ > ================================= oOo ============================== > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Sep 18 13:32:20 2002 Received: from gate3.oss.akzonobel.nl ([192.87.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IHWJw24132 for ; Wed, 18 Sep 2002 13:32:20 -0400 Received: (from fwmaster@localhost) by gate3.oss.akzonobel.nl (8.9.3a/8.6.12) id TAA03549 for ; Wed, 18 Sep 2002 19:32:01 +0200 (MET DST) Received: by gate3.oss.akzonobel.nl via smap (V1.3) id sma001145; Wed, 18 Sep 02 19:26:31 +0200 Received: by triton.oss.intra with Internet Mail Service (5.5.2653.19) id ; Wed, 18 Sep 2002 19:26:33 +0200 Message-ID: From: "Fradera, X. (Xavier)" To: "'CHEMISTRY@CCL.net'" Cc: "Mestres, J.(Jordi)" Subject: DOCK Date: Wed, 18 Sep 2002 19:25:41 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, I am using the DOCK 4.0 program for ligand-receptor docking and have found in the manual that there is a 'critical_points' parameter that can be used to make DOCK focus the search in a particular region. However, the manual does not explain how to set up the region of interest (spheres) for this kind of calculation. Anyone has used this option and can explain how to do this ? thanks. -- Xavier Fradera -------------------------------------------------------------------- This message, including attached files, may contain confidential information and is intended only for the use by the individual and/or the entity to which it is addressed. Any unauthorized use, dissemination of, or copying of the information contained herein is not allowed and may lead to irreparable harm and damage for which you may be held liable. If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete the message. -------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Sep 17 18:35:59 2002 Received: from igor.wag.caltech.edu ([131.215.26.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HMZxw23720 for ; Tue, 17 Sep 2002 18:35:59 -0400 Received: from wag.caltech.edu (DHCP-26-209.wag.caltech.edu [131.215.26.209]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id PAA1237457 for ; Tue, 17 Sep 2002 15:35:58 -0700 (PDT) Message-ID: <3D87AE4F.7050401@wag.caltech.edu> Date: Tue, 17 Sep 2002 15:35:59 -0700 From: Rick Muller User-Agent: Mozilla/5.0 (Macintosh; U; PPC Mac OS X; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PyQuante v1.03: Python Code for Quantum Chemistry (GPL) Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit PyQuante is a suite of programs for writing quantum chemistry software. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed. The resulting code is not nearly as fast as Jaguar, Gaussian, or GAMESS, but the resulting code is much easier to understand and modify. The goal of this software is not necessarily to provide a working quantum chemistry program (although it will hopefully do that), but rather to provide a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write everything. The program is released under the GNU General Public License and is thus freeware. PyQuante can be downloaded from http://pyquante.sourceforge.net. People can subscribe to the pyquante-users mailing list at http://lists.sourceforge.net/lists/listinfo/pyquante-users Here is an example of what the closed-shell Hartree-Fock scripts look like: (best viewed in a fixed-width font...) def rhf(atomlist): "General wrapper for restricted closed-shell hartree fock" from basis_631ss import basis bfs = getbasis(atomlist,basis) S,h = get1ints(bfs,atomlist) Ints = get2ints(bfs) energy = scf(atomlist,S,h,Ints) return energy def scf(atomlist,S,h,Ints,charge=0,ConvCriteria=0.0001,MaxIter=20): "Run the self-consistent field optimization of the wave function" evecs = get_guess(h,S) nel = get_nel_from_atomlist(atomlist,charge) nclosed,nopen = divmod(nel,2) enuke = get_enuke_from_atomlist(atomlist) print "nocc, enuke: ",nocc,enuke eold = 0. for i in range(MaxIter): D = mkdens(evecs,0,nocc) G = get2JmK(Ints,D) F = h+G evals,evecs = GHeigenvectors(F,S) energy = get_energy(h,F,D,enuke) print energy if abs(energy-eold) < ConvCriteria: break eold = energy return energy This is a preliminary release. Simple HF and LDA calculations work, but not much else. Still, it should be useful for people who want to learn more about how quantum chemistry calculations work. Rick From chemistry-request@server.ccl.net Wed Sep 18 13:28:58 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IHSvw24086 for ; Wed, 18 Sep 2002 13:28:58 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g8IHIom03118 for ; Wed, 18 Sep 2002 19:18:50 +0200 Message-ID: <3D88B7D3.2030107@pharma.u-strasbg.fr> Date: Wed, 18 Sep 2002 19:28:51 +0200 From: Antoine Logean User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr-FR; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: fr-fr MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:protein side-chain Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Xavier, Side-chain modeling consists mainly in the right choice of dihedral angles, Xi i = 1,2,3 and 4. Bond lengths and bond angles stay (more or less) constant and can be taken from force field parameters. Statistical studies attempting to determine the distribution of side chain dihedral values of a subset of the PDB permitted to define mainly two different kind of rotamer libraries : Backbone dependent-rotamer library : Dunbrack, R.L., Jr. and M. Karplus, Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol, 1993. 230(2): p. 543-74. and his web site : http://www.fccc.edu/research/labs/dunbrack/bbdep.html Backbone-independent rotamer library : Lovell, S.C., et al., The penultimate rotamer library. Proteins, 2000. 40(3): p. 389-408. other references : Summers, N.L. and M. Karplus, Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin. J Mol Biol, 1989. 210(4): p. 785-811. Summers, N.L. and M. Karplus, Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. J Mol Biol, 1990. 216(4): p. 991-1016. McGregor, M.J., S.A. Islam, and M.J. Sternberg, Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol, 1987. 198(2): p. 295-310. Bower, M.J., F.E. Cohen, and R.L. Dunbrack, Jr., Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol, 1997. 267(5): p. 1268-82. good work, Antoine From chemistry-request@server.ccl.net Mon Sep 16 21:22:14 2002 Received: from web9601.mail.yahoo.com ([216.136.129.180]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8H1MEw28368 for ; Mon, 16 Sep 2002 21:22:14 -0400 Message-ID: <20020917012213.41168.qmail@web9601.mail.yahoo.com> Received: from [132.207.14.8] by web9601.mail.yahoo.com via HTTP; Tue, 17 Sep 2002 03:22:13 CEST Date: Tue, 17 Sep 2002 03:22:13 +0200 (CEST) From: =?iso-8859-1?q?Mohamed=20Layachi?= Subject: need help To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-21285527-1032225733=:40532" Content-Transfer-Encoding: 8bit --0-21285527-1032225733=:40532 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hi every body i am a student in genie electric departement at montreal university . I am studing transport electric through organic molecules. And i am using a DFT method . So in my calculation i need a basis set with ECP.of gold . if some one can help me . thank you Layachi M. --------------------------------- Yahoo! Mail -- Une adresse @yahoo.fr gratuite et en français ! --0-21285527-1032225733=:40532 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

hi every body

i am a student in genie electric departement at montreal university . I am studing transport electric through organic molecules. And i am using a DFT method . So in my calculation i need a basis set with ECP.of gold . if some one can help me .

thank you  

Layachi M.


Yahoo! Mail -- Une adresse @yahoo.fr gratuite et en français !
--0-21285527-1032225733=:40532-- From chemistry-request@server.ccl.net Tue Sep 17 12:17:37 2002 Received: from doarim.bgu.ac.il ([132.72.138.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HGHaw17382 for ; Tue, 17 Sep 2002 12:17:36 -0400 Received: from gatekeeper1.bgu.ac.il ([132.72.138.92]) by doarim.bgu.ac.il with ESMTP id <20020917161735.CCHY15728.doarim@gatekeeper1.bgu.ac.il> for ; Tue, 17 Sep 2002 19:17:35 +0300 Received: from gatekeeper1.bgu.ac.il (localhost [127.0.0.1]) by gatekeeper1.bgu.ac.il (8.9.3/8.9.3) with ESMTP id SAA29930 for ; Tue, 17 Sep 2002 18:16:22 +0200 (IST) From: ilfir@bgumail.bgu.ac.il Received: from ERA ([132.72.170.150]) by gatekeeper1.bgu.ac.il (8.9.3/8.9.3) with ESMTP id SAA29923 for ; Tue, 17 Sep 2002 18:16:22 +0200 (IST) Date: Tue, 17 Sep 2002 19:19:12 +0200 X-Mailer: The Bat! (v1.47 Halloween Edition) UNREG / CD5BF9353B3B7091 Reply-To: ilfir@bgumail.bgu.ac.il X-Priority: 3 (Normal) Message-ID: <11937197533.20020917191912@bgumail.bgu.ac.il> To: chemistry@ccl.net Subject: summary: fluorescence lifetime calculation Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hello, It is summary of replies on my question that was sent one week ago: Initial question was: "I am interested in prediction of fluorescence lifetime of organic molecules. Is there any reasonable approach to calculate this value or make approximate estimation. I suppose I may use difference of energies between ground and exited singlet state. Please send on my mail as I am not subscriber. Thank you." I took several answers (thank you very much!!!) those are very promising (!): ******************************************************* 1. "Najeeb Said" : Although some semi-empirical methods allow you to predict wavelength of a photon emitted from the excited state (http://www.accelrys.com/cerius2/zindo.html), these methods will not tell you if an efficient non-radiative relaxation pathway to the ground state is present e.g. cis/trans isomerisation or electron transfer. Ab-initio calculations on the excited state are required to determine this and these are computationally expensive. As an example see (Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines; Sanchez-Galvez, A et al; J. Am. Chem. Soc., 122 (12), 2911 -2924, 2000). The calculation of fluorescence lifetime is an even more challenging area. As I mentioned earlier, depopulation of the excited state can occur by via fluorescence, internal conversion, electron transfer and other processes. These competing processes can be described as a series of rate constants i.e. K(depop) = K(fluorescence) + K(non-fluorescence) Where K(non-fluorescence) = K(internal conversion) + K(electron transfer) + K(other pathways). To determine the fluorescent lifetime (1/ Kfluorescence) of a compound, you would need to follow the trajectory of its excited state along a reaction co-ordinate (time). When you consider that a typical organic dye has a fluorescent lifetime in the nanosecond region and a typical timestep in these calculations is in the fentosecond scale (Jolibois, F et al. J. Am. Chem. Soc.; 2000; 122; 5801-5810), the calculation of fluorescent lifetimes of organic dyes is beyond our capabilities. The area of fluorescence modelling is a fascinating, but challenging area. Can you please send a summary of your answers to this list. Regards, Najeeb Said ================= Amersham Biosciences The Maynard Centre Cardiff, UK ******************************************************* 2. Sergei Tretiak Hi Ifir, You could calculate the radiative lifetime "tau" with formulae k_rad=4/3 * E^3 d^2/c^3 where k is the radiative decay rate (1/tau), c is the speed of light, E is the difference between ground and exited singlet state energies and d is the transition dipole moment associated with this transition. Practical expression is tau[ns]=6000/d^2[Debye]/E^3[eV] The transition dipole is well defined, it is dipole moment associated with optical transition between states, i.e. d_ge=<\psi_e| D | \psi_g>, where \psi_e and \psi_g are excited and ground state electronic wavefunctions and D is the dipole moment operator (note that you have x, y and z components of d and their vector's sum). It does not associated with ground or excited state dipoles given by d_gg=<\psi_g| D | \psi_g > and d_ee=<\psi_e| D | \psi_e >, but closely related to the oscillator strength f for a given optical transition f=2/3 * d^2 * E_e, where E_e is the transition frequency. Note that this way you are going to calculate the radiative decay rate only, internal conversion (e.g. to triplet), energy and electron transfer channels will not be accounted for. The total depopulation rate would be the sum of all these rates. Best, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Theoretical Division | Voice: (505) 667-8351 | | Mail stop B262 | Fax: (505) 665-4063 | | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| ******************************************************* 3. Qadir (Centre de Recherche en de Modélisation Moléculaire) Well, the problem is really complicated, and one can not really get anything from considering just energies between ground and exited states. At least you have to consider transition moments and the energy gap (i.e. one needs to calculate the oscillator strength, which is something like f=1/3*TD^2*deltaE). Using this may be you can make some correlations between fluorescence lifetime and calculated properties. I am sure there are some rigorous way to calculate fluorescence lifetime but I don't think it is too easy... ******************************************************* Ok, now I see there is practical approach to the problem. It should be tried! If anyone will have good experience with with expression please send message to this board and to me. Best regards, Ilfir mailto:ilfir@bgumail.bgu.ac.il http://ilfir.cjb.net From chemistry-request@server.ccl.net Mon Sep 16 22:39:12 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8H2dCw29949 for ; Mon, 16 Sep 2002 22:39:12 -0400 Received: from laval.chem.ucsb.edu (laval.chem.ucsb.edu [128.111.116.56]) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id g8H2d0jS012288 for ; Mon, 16 Sep 2002 19:39:00 -0700 (PDT) Date: Mon, 16 Sep 2002 19:38:48 -0700 (PDT) From: Andrij Baumketner X-X-Sender: andrij@localhost.localdomain To: chemistry@ccl.net Subject: CHARMM: Is there any problem with velocity Verlet in c28b2 ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Dear CCLers, I am trying to simulate a short peptide fully solvated in TIP3 water by using 28beta2 version of CHARMM. I intend to employ constant NVT conditions and, although the system under study is not particularly large, I need a parallel implementation of the code. As far as I understand, in CHARMM the NVT ensemble can only be generated in parallel by using velocity version (VVER key) of the Verlet algorithm combined with the Nose-Hoover thermostat. (I could probably use CPT but I'm not sure about how scaling of coordinates is dealt with there). When running a short simulation on a fully equilibrated system I find that: a) VVER version produces considerably lower potential energy than the original Verlet (non-parallel) algorithm when the SHAKE is applied. The non-parallel Verlet gives results consistent with the CPT ensemble simulations. b) if SHAKE is not applied the VVER algorithm just goes unstable. It pumps all the energy into vibrations of both solute and solvent molecules until the algorithm breaks. The original Verlet works just fine under the same conditions. I would appreciate any comments or suggestions from those who have encounter these problems before. With best wishes, Andrij -- ========================================= A. Baumketner Postdoctoral Fellow Department of Chemistry and Biochemistry University of California at Santa Barbara Santa Barbara, CA 93106, USA Tel: +1-805-252-2611 Fax: +1-805-893-4120 ========================================= From chemistry-request@server.ccl.net Tue Sep 17 19:02:29 2002 Received: from anchor-post-39.mail.demon.net ([194.217.242.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HN2Tw25695 for ; Tue, 17 Sep 2002 19:02:29 -0400 Received: from mooncott.demon.co.uk ([158.152.180.96]) by anchor-post-39.mail.demon.net with smtp (Exim 3.36 #2) id 17rRMS-0002xO-0U for chemistry@ccl.net; Wed, 18 Sep 2002 00:02:28 +0100 Message-ID: Date: Wed, 18 Sep 2002 00:01:19 +0100 To: chemistry@ccl.net From: Roger Hull Subject: Re: CCL:Autodock on Windows? References: <001301c25a6d$2f049600$0300a8c0@attbi.com> In-Reply-To: <001301c25a6d$2f049600$0300a8c0@attbi.com> MIME-Version: 1.0 X-Mailer: Turnpike Integrated Version 4.02 U Mark, Yes, I have been able to compile Autodock 3.0.5 (with minimal changes to the source code but quite a lot of changes to the make files) with MS Visual c++ v6 to run under UWIN v2.9 (available free for academic use). I'm told that the modified files also work for Cygwin. In my tests on a laptop with 64M RAM, the UWIN version under Windows 2000 runs about 30% slower than the linux version on the same machine, but this may be because Win2K does not handle virtual memory as well as linux. If anyone wants instructions for converting the files, please e-mail me and I will send them to you (MS Word format). I don't feel free to distribute the modified files without the risk of breaking the Autodock licence terms, but you are welcome to the (quite detailed) instructions! Roger Hull. In article <001301c25a6d$2f049600$0300a8c0@attbi.com>, Mark Thompson writes > >Has anyone compiled/converted AutoDock 3.x to run on Windows? > >Mark > >================================= >Mark Thompson, Ph.D. >Planaria Software >PO Box 55207 >Seattle, WA 98155 > >http://www.arguslab.com >FAX: 206-440-3305 >================================= From chemistry-request@server.ccl.net Wed Sep 18 09:58:01 2002 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IDw0w18991 for ; Wed, 18 Sep 2002 09:58:00 -0400 Received: from cosmologic.de (xdsl-195-14-220-234.netcologne.de [195.14.220.234]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id BNO95645; Wed, 18 Sep 2002 15:57:29 +0200 (CEST) Message-ID: <3D888646.E2D2FEE@cosmologic.de> Date: Wed, 18 Sep 2002 15:57:26 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Ng Man Fai CC: CHEMISTRY@ccl.net Subject: Re: CCL:Onsager equation References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The problem is not so simple. Read my paper "Calculation of UV/Vis Spectra in Solution" J.Phys.Chem. 1996, 100, 3349 Andreas Ng Man Fai schrieb: > > Hi, may I ask that how to implement the Onsager equation for calculating > the solvent effect in the excited state calculations? I have changed the > ground state fock matrix by adding the dielectric term, but where to put > the index of refraction term? > > Best regards, > Andy > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 18 09:21:32 2002 Received: from doarim.bgu.ac.il ([132.72.138.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IDLSw17972 for ; Wed, 18 Sep 2002 09:21:29 -0400 Received: from gatekeeper1.bgu.ac.il ([132.72.138.92]) by doarim.bgu.ac.il with ESMTP id <20020918132124.ELBI15728.doarim@gatekeeper1.bgu.ac.il> for ; Wed, 18 Sep 2002 16:21:24 +0300 Received: from gatekeeper1.bgu.ac.il (localhost [127.0.0.1]) by gatekeeper1.bgu.ac.il (8.9.3/8.9.3) with ESMTP id PAA07789 for ; Wed, 18 Sep 2002 15:20:11 +0200 (IST) From: ilfir@bgumail.bgu.ac.il Received: from ERA ([132.72.170.150]) by gatekeeper1.bgu.ac.il (8.9.3/8.9.3) with ESMTP id PAA07785 for ; Wed, 18 Sep 2002 15:20:11 +0200 (IST) Date: Wed, 18 Sep 2002 16:22:58 +0200 X-Mailer: The Bat! (v1.47 Halloween Edition) UNREG / CD5BF9353B3B7091 Reply-To: ilfir@bgumail.bgu.ac.il X-Priority: 3 (Normal) Message-ID: <16226709298.20020918162258@bgumail.bgu.ac.il> To: chemistry@ccl.net Subject: summary: fluorescence lifetime calculation Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hello, It is summary of replies on my question that was sent one week ago: Initial question was: "I am interested in prediction of fluorescence lifetime of organic molecules. Is there any reasonable approach to calculate this value or make approximate estimation. I suppose I may use difference of energies between ground and exited singlet state. Please send on my mail as I am not subscriber. Thank you." I took several answers (thank you very much!!!) those are very promising (!): ******************************************************* 1. "Najeeb Said" : Although some semi-empirical methods allow you to predict wavelength of a photon emitted from the excited state (http://www.accelrys.com/cerius2/zindo.html), these methods will not tell you if an efficient non-radiative relaxation pathway to the ground state is present e.g. cis/trans isomerisation or electron transfer. Ab-initio calculations on the excited state are required to determine this and these are computationally expensive. As an example see (Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines; Sanchez-Galvez, A et al; J. Am. Chem. Soc., 122 (12), 2911 -2924, 2000). The calculation of fluorescence lifetime is an even more challenging area. As I mentioned earlier, depopulation of the excited state can occur by via fluorescence, internal conversion, electron transfer and other processes. These competing processes can be described as a series of rate constants i.e. K(depop) = K(fluorescence) + K(non-fluorescence) Where K(non-fluorescence) = K(internal conversion) + K(electron transfer) + K(other pathways). To determine the fluorescent lifetime (1/ Kfluorescence) of a compound, you would need to follow the trajectory of its excited state along a reaction co-ordinate (time). When you consider that a typical organic dye has a fluorescent lifetime in the nanosecond region and a typical timestep in these calculations is in the fentosecond scale (Jolibois, F et al. J. Am. Chem. Soc.; 2000; 122; 5801-5810), the calculation of fluorescent lifetimes of organic dyes is beyond our capabilities. The area of fluorescence modelling is a fascinating, but challenging area. Can you please send a summary of your answers to this list. Regards, Najeeb Said ================= Amersham Biosciences The Maynard Centre Cardiff, UK ******************************************************* 2. Sergei Tretiak Hi Ifir, You could calculate the radiative lifetime "tau" with formulae k_rad=4/3 * E^3 d^2/c^3 where k is the radiative decay rate (1/tau), c is the speed of light, E is the difference between ground and exited singlet state energies and d is the transition dipole moment associated with this transition. Practical expression is tau[ns]=6000/d^2[Debye]/E^3[eV] The transition dipole is well defined, it is dipole moment associated with optical transition between states, i.e. d_ge=<\psi_e| D | \psi_g>, where \psi_e and \psi_g are excited and ground state electronic wavefunctions and D is the dipole moment operator (note that you have x, y and z components of d and their vector's sum). It does not associated with ground or excited state dipoles given by d_gg=<\psi_g| D | \psi_g > and d_ee=<\psi_e| D | \psi_e >, but closely related to the oscillator strength f for a given optical transition f=2/3 * d^2 * E_e, where E_e is the transition frequency. Note that this way you are going to calculate the radiative decay rate only, internal conversion (e.g. to triplet), energy and electron transfer channels will not be accounted for. The total depopulation rate would be the sum of all these rates. Best, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Theoretical Division | Voice: (505) 667-8351 | | Mail stop B262 | Fax: (505) 665-4063 | | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| ******************************************************* 3. Qadir (Centre de Recherche en de Modélisation Moléculaire) Well, the problem is really complicated, and one can not really get anything from considering just energies between ground and exited states. At least you have to consider transition moments and the energy gap (i.e. one needs to calculate the oscillator strength, which is something like f=1/3*TD^2*deltaE). Using this may be you can make some correlations between fluorescence lifetime and calculated properties. I am sure there are some rigorous way to calculate fluorescence lifetime but I don't think it is too easy... ******************************************************* Ok, now I see there is practical approach to the problem. It should be tried! If anyone will have good experience with with expression please send message to this board and to me. Best regards, Ilfir mailto:ilfir@bgumail.bgu.ac.il http://ilfir.cjb.net From chemistry-request@server.ccl.net Wed Sep 18 04:26:31 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8I8QUw11129 for ; Wed, 18 Sep 2002 04:26:30 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g8I8GLm23801; Wed, 18 Sep 2002 10:16:21 +0200 Message-ID: <3D8838AC.50905@pharma.u-strasbg.fr> Date: Wed, 18 Sep 2002 10:26:20 +0200 From: Antoine Logean User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr-FR; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: fr-fr MIME-Version: 1.0 To: Xavier Gallet , "'chemistry@ccl.net'" Subject: Re: CCL:protein side-chains References: <200209171052.25581.gallet@genodyssee.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, Side-chain modeling consists mainly in the right choice of dihedral angles, Xi i = 1,2,3 and 4. Bond lengths and bond angles stay (more or less) constant and can be taken from force field parameters. Statistical studies establishing distribution of dihedral values in a subset of the PDB give rise to different rotamer libraries : Backbone dependent-rotamer library : Dunbrack, R.L., Jr. and M. Karplus, Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol, 1993. 230(2): p. 543-74. and his web site : http://www.fccc.edu/research/labs/dunbrack/bbdep.html Backbone-independent rotamer library : Lovell, S.C., et al., The penultimate rotamer library. Proteins, 2000. 40(3): p. 389-408. and : Summers, N.L. and M. Karplus, Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin. J Mol Biol, 1989. 210(4): p. 785-811. Summers, N.L. and M. Karplus, Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. J Mol Biol, 1990. 216(4): p. 991-1016. McGregor, M.J., S.A. Islam, and M.J. Sternberg, Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol, 1987. 198(2): p. 295-310. Bower, M.J., F.E. Cohen, and R.L. Dunbrack, Jr., Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol, 1997. 267(5): p. 1268-82. good work Antoine From chemistry-request@server.ccl.net Mon Sep 16 07:31:07 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GBV6w02739 for ; Mon, 16 Sep 2002 07:31:06 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g8GBV6U3017645 for ; Mon, 16 Sep 2002 08:31:06 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Mon Sep 16 08:31:06 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA01514 for ; Mon, 16 Sep 2002 08:31:05 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Mon, 16 Sep 2002 08:31:04 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Distributed Computing and Autodock: Summary Message-ID: <3D85C339@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Thanks to Christoph and V. Mohan for replying to my question about distributed computing and autodock. My original question with their replies are given below. Robert Question: CCL Users, I'm wondering if anyone knows if it is possible to perform docking using Autodock on a cluster of networked computers connected by a 10/100 ethernet. I read that Autodock 3.0 was capable of running this way (J. Comput. Chem., 1998, Vol 19(14):1639-1662), however, I may be mistaken. I have not been able to find anything else about this capability of Autodock. Has anyone ever been able to run Autodock like this, and if so, what is involved? Must Autodock be installed on each processor? I will summarize the responses to the list. Thanks, Robert Replies: assuming thast you have N ligands to dock and M computers at your disposal, and a NFS-mounted irectory from which you can run and all your input prepared (this is the hard part). Use something like the following csh script fragment: @ count = 0 while ($count < N) foreach computer ( insert your computer names here ) rsh $computer "script_to_start_autodock" filename$count @ count = $count + 1 end end A real version will need some safeguards and other bells and whistles, but the basic logic is there. You really only need to control the execution of N autodock runs and make sure they all use the correct input and produce unique output files. Cheers, Christoph | Dr. Christoph Weber Sen. Applications Specialist | Research Computing, TPC21 858-784-9869 (phone) | The Scripps Research Institute 858-784-9301 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~weber/ Trust the computer industry to shorten 'Year 2000' to 'Y2K'. It was this kind of thinking that caused the problem in the first place Hi, Yes, it is possible to run in the mode you're talking about. I've seen some information to that effect, on a number of grid computing companies webpages. For example, you should check www.entropia.com Equivalent to SETI@home type projects, fight_AIDS@home [running Autodock on a massive number of PCs] have been documented. ---- V. Mohan Ph.D. Research Fellow 3-Dimensional Pharmaceuticals 8 Clarke Drive Cranbury NJ 08512 Tel: 609 655 6934 ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** From chemistry-request@server.ccl.net Mon Sep 16 04:40:07 2002 Received: from gatekeeper.tripos.com (firewall-user@[192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8G8e6w32182 for ; Mon, 16 Sep 2002 04:40:06 -0400 Received: (from uucp@localhost) by gatekeeper.tripos.com (8.11.6+Sun/8.11.6) id g8G8e0I02587 for ; Mon, 16 Sep 2002 03:40:00 -0500 (CDT) Received: from cairo.tripos.com(172.20.176.21) by gatekeeper.tripos.com via csmap (V6.0) id srcAAAgAaidf; Mon, 16 Sep 02 03:39:58 -0500 Received: (from nmalcolm@localhost) by cairo.tripos.com (SGI-8.9.3/8.9.3) id HAA37506; Mon, 16 Sep 2002 07:40:31 -0100 (BST) Date: Mon, 16 Sep 2002 07:40:31 -0100 (BST) Message-Id: <200209160840.HAA37506@cairo.tripos.com> X-Authentication-Warning: cairo.tripos.com: nmalcolm set sender to nmalcolm@tripos.com using -f From: "Nathaniel O.J. Malcolm" To: marczerw@rutchem.rutgers.edu CC: chemistry@ccl.net In-reply-to: <3D7F6652.74ABC984@rutchem.rutgers.edu> (message from Margaret Czerw on Wed, 11 Sep 2002 11:50:42 -0400) Subject: Re: CCL:input orientation Sender: nmalcolm@tripos.com Reply-To: nmalcolm@tripos.com Organization: Tripos UK Ltd. References: <3D7F6652.74ABC984@rutchem.rutgers.edu> Margret, Not sure if you have already solved this problem, but just in case you haven't.... If you use "Opt=z-matrix" and "nosymm" in your input then you should be able to retain an initial orientation. However you will have to be very careful in setting up your Z-matrix so that the coordinates you are interested in are defined first. Noj -- -------------------------------- Dr. N.O.J. Malcolm Software Application Scientist Tripos UK Ltd nmalcolm@tripos.com Tel +44 (0)1908 650020 Fax +44 (0)1908 650001 -------------------------------- Sybyl, Unity and other products are exclusive property of Tripos & are protected trademarks, copyrights, & patents as appropriate The information in this e-mail is confidential and may have associated legal obligations. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender. From chemistry-request@server.ccl.net Tue Sep 17 06:11:22 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HABMw09463 for ; Tue, 17 Sep 2002 06:11:22 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H2K00IA8UWEW5@mailstudenti.unimi.it> for chemistry@ccl.net; Tue, 17 Sep 2002 12:09:51 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H2K007CCUWF43@smtp.unimi.it> for chemistry@ccl.net; Tue, 17 Sep 2002 12:09:52 +0200 (MEST) Date: Tue, 17 Sep 2002 12:17:11 +0200 From: Giulio Vistoli Subject: Re: CCL:autodock To: Venkataraman Kabaleeswaran , chemistry@ccl.net Message-id: <001101c25e33$62f60ab0$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <200209162247.g8GMlD504373@medusa.wo.utoledo.edu> dear venkataraman, In order to convert pdb to mol2 and/or pdbq you can use VEGA software (http://users.unimi.it/ddl) that is able to convert several file formats in mol2 or pdbq assigning atomic charges and atom types. Best regards Giulio ---------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Sun Sep 15 18:00:16 2002 Received: from web13509.mail.yahoo.com ([216.136.173.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8FM0Gw07228 for ; Sun, 15 Sep 2002 18:00:16 -0400 Message-ID: <20020915220015.33213.qmail@web13509.mail.yahoo.com> Received: from [130.74.167.214] by web13509.mail.yahoo.com via HTTP; Sun, 15 Sep 2002 15:00:15 PDT Date: Sun, 15 Sep 2002 15:00:15 -0700 (PDT) From: Subject: How does one go about finding postdoc positions in Institutions? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello All, Does anyone know of good websites or a good way in which you can get a list of the available postdoctoral positions all over the world. esp. Europe. Thank you Yogesh Sabnis __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From chemistry-request@server.ccl.net Mon Sep 16 10:09:34 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GE9Yw06159 for ; Mon, 16 Sep 2002 10:09:34 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g8GE9WU3009143 for ; Mon, 16 Sep 2002 11:09:33 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Mon Sep 16 11:09:31 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id LAA09766 for ; Mon, 16 Sep 2002 11:09:31 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Mon, 16 Sep 2002 11:09:30 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Distributed Computing and Autodock: Summary Message-ID: <3D8652F5@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Sorry, I'm resending this summary because I forgot the reply from David. Thanks to Christoph, David, and V. Mohan for replying to my question about distributed computing and autodock. My original question with their replies are given below. Robert Question: CCL Users, I'm wondering if anyone knows if it is possible to perform docking using Autodock on a cluster of networked computers connected by a 10/100 ethernet. I read that Autodock 3.0 was capable of running this way (J. Comput. Chem., 1998, Vol 19(14):1639-1662), however, I may be mistaken. I have not been able to find anything else about this capability of Autodock. Has anyone ever been able to run Autodock like this, and if so, what is involved? Must Autodock be installed on each processor? I will summarize the responses to the list. Thanks, Robert Replies: assuming thast you have N ligands to dock and M computers at your disposal, and a NFS-mounted directory from which you can run and all your input prepared (this is the hard part). Use something like the following csh script fragment: @ count = 0 while ($count < N) foreach computer ( insert your computer names here ) rsh $computer "script_to_start_autodock" filename$count @ count = $count + 1 end end A real version will need some safeguards and other bells and whistles, but the basic logic is there. You really only need to control the execution of N autodock runs and make sure they all use the correct input and produce unique output files. Cheers, Christoph | Dr. Christoph Weber Sen. Applications Specialist | Research Computing, TPC21 858-784-9869 (phone) | The Scripps Research Institute 858-784-9301 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~weber/ Trust the computer industry to shorten 'Year 2000' to 'Y2K'. It was this kind of thinking that caused the problem in the first place Hi, Yes, it is possible to run in the mode you're talking about. I've seen some information to that effect, on a number of grid computing companies webpages. For example, you should check www.entropia.com Equivalent to SETI@home type projects, fight_AIDS@home [running Autodock on a massive number of PCs] have been documented. ---- V. Mohan Ph.D. Research Fellow 3-Dimensional Pharmaceuticals 8 Clarke Drive Cranbury NJ 08512 Tel: 609 655 6934 just run different jobs on each processor. Much more efficient than parallellizing AD. You can work on the same problem by starting all of the jobs with a different random seed. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** From chemistry-request@server.ccl.net Wed Sep 18 17:02:35 2002 Received: from copland.udel.edu ([128.175.13.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IL2Yw29717 for ; Wed, 18 Sep 2002 17:02:34 -0400 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.9.3/8.9.3) with ESMTP id RAA00479 for ; Wed, 18 Sep 2002 17:02:34 -0400 (EDT) Message-Id: <200209182102.RAA00479@copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Wed, 18 Sep 2002 16:42:01 -0400 Subject: IR-spectra from G98 outputs From: "Olga Dmitrenko" To: chemistry@ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, Does anyone know the most time-economic way to convert frequency/intensity data > from the g98 output file into 2-column data set for the IR-spectrum picture? Maybe some script exists for getting two columns: X=freqs and Y=IR Inten? I am using grep and then Excel for these conversions, but when the molecule is getting bigger, my Excel exercises become very time-consuming. Thanks ******************************************* * Dr. Olga Dmitrenko * Department of Chemistry and Biochemistry * University of Delaware, Newark * Delaware 19716, USA * Ph. (302) 831-0887 * Fax. (302) 831-6335 * E-mail: odmitr@udel.edu ******************************************* From chemistry-request@server.ccl.net Mon Sep 16 06:19:43 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GAJgw01673 for ; Mon, 16 Sep 2002 06:19:43 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 17r1Or-0004hD-00 for chemistry@ccl.net; Mon, 16 Sep 2002 12:19:13 -0700 Date: Mon, 16 Sep 2002 11:26:15 +0200 (CEST) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: chemistry@ccl.net Subject: molecular surface - properties Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dears CCL users, I need a software capable to calculate the value of some properties ( like electrostatic potential, IE, and other) on molecular surface. I need that the output of this program is a file in which the value for a property is written for all molecular surface's points Do you know something like this? -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it Prima ti ignorano. Poi ridono di te. Poi ti combattono. Poi tu vinci. From chemistry-request@server.ccl.net Mon Sep 16 11:08:52 2002 Received: from ns.ice.mpg.de ([195.37.47.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8GF8pw07285 for ; Mon, 16 Sep 2002 11:08:51 -0400 Received: from [10.10.11.61] (helo=ice.mpg.de) by ns.ice.mpg.de with esmtp (Exim 3.14 #17) id 17qxUY-00057s-00; Mon, 16 Sep 2002 17:08:50 +0200 Message-ID: <3D85F3FB.6060108@ice.mpg.de> Date: Mon, 16 Sep 2002 17:08:43 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max Planck Institute of Chemical Ecology User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Chunhui Li CC: chemistry@ccl.net Subject: Re: CCL:linear code to 2D or 3D structure References: <5.1.0.14.2.20020913123611.00a917c0@lulu.it.northwestern.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Chunhui Li wrote: > Hi, > > if I only have bond connectivity information without coordinates for > many molecules, is there any software I can use to get the 2D or 3D > structure without drawing? The Chemistry Development Kit (CDK) is an open-source Java library for structural chemo- and bioinformatics. It has a SMILES parser and a Structure Diagram Generator, which enables you to generate 2D coordinates for molecular graphs. The software with source code and documentation can be found under http://cdk.sourceforge.net Feel free to email to cdk-devel@lists.sf.net if you need assistance with using the code. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Wed Sep 18 18:20:54 2002 Received: from mtiwmhc22.worldnet.att.net ([204.127.131.47]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IMKsw31912 for ; Wed, 18 Sep 2002 18:20:54 -0400 Received: from dopetec ([138.23.156.82]) by mtiwmhc22.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020918222049.HMOP15630.mtiwmhc22.worldnet.att.net@dopetec> for ; Wed, 18 Sep 2002 22:20:49 +0000 Message-ID: <000a01c25f61$a5137f20$529c178a@dopetec> From: "Donald Keidel" To: Subject: CPU-hours on supercomputer vs. PC hours Date: Wed, 18 Sep 2002 15:20:49 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C25F26.F7D93B40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C25F26.F7D93B40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I am applying for computer time through an NPACI allocation and I have a = question regarding CPU-hours or as they call them SUs. If anyone on the = CCL has had computer time before and knows how to convert between hours = it takes to complete a Gaussian calculation on a PC (linux) and hours it = might take to complete the same calculation on a NPACI computer please = let me know. I do not want to ask for too many hours or too little. = Any help is appreciated. Thank you very much in advance. Don -------------------------------------------------------------------------= -------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0007_01C25F26.F7D93B40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
 
I am applying for computer time through = an NPACI=20 allocation and I have a question regarding CPU-hours or as they call = them=20 SUs.  If anyone on the CCL has had computer time before and knows = how to=20 convert between hours it takes to complete a Gaussian calculation on a = PC=20 (linux) and hours it might take to complete the same calculation on a = NPACI=20 computer please let me know.  I do not want to ask for too many = hours or=20 too little.  Any help is appreciated.  Thank you very much in=20 advance.
 
Don
 
----------------------------------------------------------------= -----------------------------------------------
Donald=20 J. Keidel
University of California, Riverside
Department of = Biochemistry=20 and Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /FONT>
 
 
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