From chemistry-request@server.ccl.net Wed Nov 7 00:46:42 2001 Received: from smtp.dicp.ac.cn ([159.226.159.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA75kfB32497 for ; Wed, 7 Nov 2001 00:46:41 -0500 Received: from congyao ([159.226.159.204]) by smtp.dicp.ac.cn (8.11.6/8.11.6) with SMTP id fA75nna18089 for ; Wed, 7 Nov 2001 13:49:49 +0800 Message-Id: <200111070549.fA75nna18089@smtp.dicp.ac.cn> Date: Wed, 7 Nov 2001 13:49:33 +0800 From: wangyanemail To: "CHEMISTRY@ccl.net" Subject: about nanometer scale calculation X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit CHEMISTRYDear CCLers: hello,I want to research nanometer scale calculation on metals(for example Ag) or catalysts. Would you like to tell me : 1.which softwares suit to it ? 2 which research groups are working on it? 3 some literatures and advice on it. If one can give me some advice or information about nanometer scale calculation on metals or catalysts, I'll appreciate him very much. wangyanemail wangyanemail@dicp.ac.cn From chemistry-request@server.ccl.net Tue Oct 30 15:47:23 2001 Received: from ns02.sbphrd.com (firewall-user@[208.198.64.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9UKkrB03533 for ; Tue, 30 Oct 2001 15:47:23 -0500 Received: by ns02.sbphrd.com; id PAA18875; Tue, 30 Oct 2001 15:49:40 -0500 (EST) From: Received: from unknown(139.136.64.5) by ns02.sbphrd.com via smap (V5.0) id xma018838; Tue, 30 Oct 01 15:49:27 -0500 Received: from uksmtp01.ha.uk.sbphrd.com (uksmtp01.ha.uk.sbphrd.com [139.136.216.185]) by phinet.sbphrd.com (8.9.1b+Sun/8.9.1) with ESMTP id PAA22696; Tue, 30 Oct 2001 15:49:33 -0500 (EST) To: biopython-announce-l@biopython.org, chemweb@ic.ac.uk, bioinformatics@sdsc.edu, tc@omg.org, lifesciences@omg.org, chemistry@ccl.net Subject: Life Sciences Standards for the 21st Century X-Mailer: Lotus Notes Release 5.0.3 (Intl) 21 March 2000 Message-ID: Date: Tue, 30 Oct 2001 15:48:42 -0500 X-MIMETrack: Serialize by Router on UKSMTP01/SERVERS/PHRD/SB_PLC(Release 5.0.5 |September 22, 2000) at 30/10/2001 20:49:26, Serialize complete at 30/10/2001 20:49:26 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 0072521585256AF5_=" This is a multipart message in MIME format. --=_alternative 0072521585256AF5_= Content-Type: text/plain; charset="us-ascii" [with apologies to everyone who receives more copies of this invitation than desired] Colleagues: Five minutes to change the world (of life science software)! The OMG Life Sciences Research (LSR) Domain Task Force (see: http://lsr.omg.org) provides an open forum for the collaborative development of standards and specifications to support software and information interoperation. To date, the LSR has developed standards for (and LSR members and others have developed implementations of) sequence analysis, genomic maps, macromolecular structures, bibliographic search, and laboratory instrument control. Additional work is underway in the areas of chemical structures, gene expression, and laboratory workflow. We are interested in addressing the areas of greatest interest and need for interoperability in the life sciences research community. We have, therefore, developed a brief "Industry Survey" to seek your advice in identifying and prioritizing topics for future standards development work. This survey is intended for everyone interested in improved life sciences research software: commercial and academic; developers, vendors, and software users; OMG members and non-members. Survey answers will be kept confidential and only presented in statistical summary. So, here's how you can help create better software for life science research: please take a few minutes to go to http://lsr.ebi.ac.uk/survey/survey_form.html and give your answers to the questions there. And please share this invitation with your interested colleagues. Thank you very much, David Benton, GlaxoSmithKline, LSR Co-Chair James Fry, Pfizer, LSR Cheminformatics Working Group Co-Chair Doug Greer, San Diego Supercomputer Center, LSR Macromolecular Structure Working Group Chair Karl Konnerth, Incyte Genomics, LSR Co-Chair Scott Markel, NetGenics, LSR Co-Chair Tony Parsons, Pfizer, LSR LECIS Working Goup, Co-Chair Thorsten Richter, Creon-Lab-Control, LSR LECIS Working Goup, Co-Chair Richard Scott, De Novo Pharmaceuticals, LSR Cheminformatics Working Group Co-Chair Martin Senger, European Bioinformatics Institute, LSR Workflow Working Group Chair Torsten Staab, Los Alamos National Laboratory, LSR LECIS Working Group Co-Chair Charles Troup, Agilent, LSR Gene Expression Working Group Chair --=_alternative 0072521585256AF5_= Content-Type: text/html; charset="us-ascii"
[with apologies to everyone who receives more copies of this invitation than desired]
Colleagues:

Five minutes to change the world (of life science software)!

The OMG Life Sciences Research (LSR) Domain Task Force (see: http://lsr.omg.org) provides an open forum for the collaborative development of standards and specifications to support software and information interoperation. To date, the LSR has developed standards for (and LSR members and others have developed implementations of) sequence analysis, genomic maps, macromolecular structures, bibliographic search, and laboratory instrument control. Additional work is underway in the areas of chemical structures, gene expression, and laboratory workflow.

We are interested in addressing the areas of greatest interest and need for interoperability in the life sciences research community.  We have, therefore, developed a brief "Industry Survey" to seek your advice in identifying and prioritizing topics for future standards development work.  This survey is intended for everyone interested in improved life sciences research software: commercial and academic; developers, vendors, and software users; OMG members and non-members.  Survey answers will be kept confidential and only presented in statistical summary.

So, here's how you can help create better software for life science research:  please take a few minutes to go to http://lsr.ebi.ac.uk/survey/survey_form.html and give your answers to the questions there.  And please share this invitation with your interested colleagues.



Thank you very much,

David Benton, GlaxoSmithKline, LSR Co-Chair
James Fry, Pfizer, LSR Cheminformatics Working Group Co-Chair
Doug Greer, San Diego Supercomputer Center, LSR Macromolecular Structure Working Group Chair
Karl Konnerth, Incyte Genomics, LSR Co-Chair
Scott Markel, NetGenics, LSR Co-Chair
Tony Parsons, Pfizer,  LSR LECIS Working Goup, Co-Chair
Thorsten Richter, Creon-Lab-Control, LSR LECIS Working Goup, Co-Chair
Richard Scott, De Novo Pharmaceuticals, LSR Cheminformatics Working Group Co-Chair
Martin Senger, European Bioinformatics Institute, LSR Workflow Working Group Chair
Torsten Staab, Los Alamos National Laboratory, LSR LECIS Working Group Co-Chair
Charles Troup, Agilent, LSR Gene Expression Working Group Chair --=_alternative 0072521585256AF5_=-- From chemistry-request@server.ccl.net Wed Nov 7 00:34:54 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA75YsB32147 for ; Wed, 7 Nov 2001 00:34:54 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id AAA03186; Wed, 7 Nov 2001 00:34:53 -0500 (EST) Date: Wed, 7 Nov 2001 00:34:52 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: ALP-vibro (animate Gaussian vibs) for MS-WIN in CCL archives cc: serge@obbligato.com, Jan Labanowski Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to thank Serge for a great contribution to CCL archives: nice and small vibration animation for Gaussian files. Grab it at: http://www.ccl.net/cca/software/MS-WIN95-NT/ALP-vibro Thank you Serge!!! Jan Date: Wed, 24 Oct 2001 20:26:25 -0700 From: Obbligato Objectives Inc. To: jkl@ccl.net Subject: software for CCL: animation of vibrational modes from Gaussian 98 I would like to add this (free) software to the CCL software archive. ALP-vibro is a program for visualization/animation of the normal modes corresponding to vibrational frequencies computed by Gaussian 98. The maximum number of displayed atoms is set to 1000. You can rotate your molecule/ion in three dimensions to get a better view of molecule/vibration mode. It is a very user-friendly program. The only required input from a user is a name of the Gaussian output file and the normal mode number you want to see. Operating System: MS Windows 95/98/2000/NT System Requirements: Pentium with 32MB RAM is recommended. Regards, Serge Gorelsky York University Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Wed Nov 7 05:19:13 2001 Received: from mr4.cc.ic.ac.uk ([155.198.5.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7AJCB08899 for ; Wed, 7 Nov 2001 05:19:13 -0500 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr4.cc.ic.ac.uk with esmtp (Exim 3.31 #1) id 161Pnc-0000Qt-04 for chemistry@ccl.net; Wed, 07 Nov 2001 10:19:12 +0000 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=argon.ch.ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 161Pnb-006HvT-00; Wed, 7 Nov 2001 10:19:11 +0000 Sender: krzys@ic.ac.uk Message-ID: <3BE90A34.7202682F@argon.ch.ic.ac.uk> Date: Wed, 07 Nov 2001 10:17:24 +0000 From: Krzysztof Radacki Reply-To: k.radacki@ic.ac.uk Organization: Imperial College X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: g98: GDIIS optimization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleauges, may be some of you can me explain this funny log-file from Gaussian. I've used OPT=(...,GDIIS) to test if my molecule convert faster with this algorithm. Bellow is print-out of log file after |grep SCF Done. SCF Done: E(RB+HF-LYP) = -574.943395055 A.U. after 2 cycles SCF Done: E(RB+HF-LYP) = -574.943394769 A.U. after 16 cycles SCF Done: E(RB+HF-LYP) = -574.943392587 A.U. after 17 cycles SCF Done: E(RB+HF-LYP) = -574.943392245 A.U. after 13 cycles SCF Done: E(RB+HF-LYP) = -574.943391875 A.U. after 14 cycles SCF Done: E(RB+HF-LYP) = -574.943391822 A.U. after 12 cycles SCF Done: E(RB+HF-LYP) = -574.943391641 A.U. after 15 cycles SCF Done: E(RB+HF-LYP) = -574.943391496 A.U. after 13 cycles SCF Done: E(RB+HF-LYP) = -574.943391347 A.U. after 13 cycles SCF Done: E(RB+HF-LYP) = -574.943391321 A.U. after 10 cycles SCF Done: E(RB+HF-LYP) = -574.943391325 A.U. after 6 cycles As you ca see every step energy is higher then in previouse. I always thought that during optimization we're looking for minimum not local maximum :) OK, I know that the difference is only 0.01 kJ/mol but never the less it strange. Just to complet the picture egrep print-out with threshold values: SCF Done: E(RB+HF-LYP) = -574.943395055 A.U. after 2 cycles Step number 1 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000287 0.000015 NO RMS Force 0.000049 0.000010 NO Maximum Displacement 0.005051 0.000060 NO RMS Displacement 0.000897 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943394769 A.U. after 16 cycles Step number 2 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000150 0.000015 NO RMS Force 0.000029 0.000010 NO Maximum Displacement 0.007530 0.000060 NO RMS Displacement 0.001487 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943392587 A.U. after 17 cycles Step number 3 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000088 0.000015 NO RMS Force 0.000015 0.000010 NO Maximum Displacement 0.001598 0.000060 NO RMS Displacement 0.000309 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943392245 A.U. after 13 cycles Step number 4 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000055 0.000015 NO RMS Force 0.000010 0.000010 YES Maximum Displacement 0.002607 0.000060 NO RMS Displacement 0.000466 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391875 A.U. after 14 cycles Step number 5 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000012 0.000015 YES RMS Force 0.000005 0.000010 YES Maximum Displacement 0.000684 0.000060 NO RMS Displacement 0.000137 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391822 A.U. after 12 cycles Step number 6 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000018 0.000015 NO RMS Force 0.000005 0.000010 YES Maximum Displacement 0.001171 0.000060 NO RMS Displacement 0.000288 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391641 A.U. after 15 cycles Step number 7 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000015 0.000015 YES RMS Force 0.000004 0.000010 YES Maximum Displacement 0.000485 0.000060 NO RMS Displacement 0.000106 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391496 A.U. after 13 cycles Step number 8 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000010 0.000015 YES RMS Force 0.000003 0.000010 YES Maximum Displacement 0.000485 0.000060 NO RMS Displacement 0.000111 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391347 A.U. after 13 cycles Step number 9 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000004 0.000015 YES RMS Force 0.000001 0.000010 YES Maximum Displacement 0.000166 0.000060 NO RMS Displacement 0.000046 0.000040 NO SCF Done: E(RB+HF-LYP) = -574.943391321 A.U. after 10 cycles Step number 10 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000004 0.000015 YES RMS Force 0.000001 0.000010 YES Maximum Displacement 0.000080 0.000060 NO RMS Displacement 0.000019 0.000040 YES SCF Done: E(RB+HF-LYP) = -574.943391325 A.U. after 6 cycles Step number 11 out of a maximum of 23 Item Value Threshold Converged? Maximum Force 0.000001 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.000026 0.000060 YES RMS Displacement 0.000006 0.000040 YES Normal termination of Gaussian 98. Any comments wellcomed. regards Krzys From chemistry-request@server.ccl.net Wed Nov 7 05:25:42 2001 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7APfB09016 for ; Wed, 7 Nov 2001 05:25:42 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id LAA15447 for ; Wed, 7 Nov 2001 11:25:40 +0100 (MET) Date: Wed, 7 Nov 2001 11:25:40 +0100 (MET) Message-Id: <200111071025.LAA15447@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: line decomposition in ZINDO Hi, does anyone now how to obtain the full line decomposition in the output file > from a ZINDO calculation (original ZINDO package). For some reason it cuts it off.. Thanks in advance Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Wed Nov 7 08:20:29 2001 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7DKTB11418 for ; Wed, 7 Nov 2001 08:20:29 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id OAA02278 for ; Wed, 7 Nov 2001 14:20:26 +0100 (MET) Date: Wed, 7 Nov 2001 14:20:26 +0100 (MET) Message-Id: <200111071320.OAA02278@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: CCL:line decomposition in ZINDO Seems that the question is a little vague .. Therefore this: >Hi, > >in the output of a zindo program (INDO/s-CIS) the eigenvector is not printed entirely >with respect to the mixing of lines (line composition), i.e. if you have an eigenvalue >of e.g. 6.65 eV, I can not look at the full line decomposition (the values that >indicate in what amount the different lines account for in this excitation). When >I compare it to e.g. hyperchem, it gives only the leading contributions. In the >ZINDO output only part of these contributions is given, and often the leading >contribution is not there (not printed). > >Hope this helps >Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Wed Nov 7 07:55:13 2001 Received: from hatrack.unc.edu.ar ([170.210.248.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7CtAB10836 for ; Wed, 7 Nov 2001 07:55:12 -0500 Received: from mail.fcq.unc.edu.ar (localhost.localdomain [127.0.0.1]) by hatrack.unc.edu.ar (8.11.2/8.11.2) with ESMTP id fA7Ctv611021 for ; Wed, 7 Nov 2001 09:55:57 -0300 Received: from fisquim.fcq.unc.edu.ar (IDENT:EZtbYJ3DnPqzksqb3KfWWryKI9WkG0je@[200.16.18.154]) by mail.fcq.unc.edu.ar (8.11.2/8.11.2) with ESMTP id fA7CqDp10811 for ; Wed, 7 Nov 2001 09:52:13 -0300 Message-ID: <3BE92EA3.2080200@fisquim.fcq.unc.edu.ar> Date: Wed, 07 Nov 2001 09:52:51 -0300 From: Gustavo Velardez User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20010917 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL Subject: G98 error Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello: When I run a calculation job by using Gauss98 #p MP2 SCF(Tight) Gen 6D test Punch=(Coord,NaturalOrbital) #p Density NOSYMM GFINPUT , for phenylacetic acid (18 atoms) I met a problem. For systems like formic acid (5 atoms) everything is OK. The error message after the 18 cycle is: ---------------------------------------------------------------------------------------------------------------------- Cycle 18 Pass 1 IDiag 1: RMSU= 3.91D-09 CP: 2.86D-03 9.11D-01 1.05D+00 1.41D+00 1.57D+00 CP: 1.72D+00 1.44D+00 1.31D+00 2.06D+00 1.15D+00 CP: 1.34D+00 1.50D+00 E=-0.946614847884659D+03 Delta-E= 0.000000000999 DIIS: error= 3.79D-09 at cycle 13. Coeff: 0.624D-06-0.230D-04 0.361D-04 0.275D-03-0.562D-03-0.158D-02 Coeff: 0.463D-02 0.358D-02-0.328D-01 0.294D-01 0.123D+00-0.282D-01 Coeff:-0.110D+01 RMSDP=7.04D-09 MaxDP=4.45D-07 SCF Done: E(RHF) = -457.530737123 A.U. after 18 cycles Convg = 0.7043D-08 -V/T = 2.0002 S**2 = 0.0000 KE= 4.574219511598D+02 PE=-2.049972190518D+03 EE= 6.459353914735D+02 Leave Link 502 at Tue Nov 6 22:58:29 2001, MaxMem= 65536000 cpu: 12857.8 (Enter /user/lokal/ga98/l801.exe) Range of M.O.s used for correlation: 11 400 NBasis= 400 NAE= 36 NBE= 36 NFC= 10 NFV= 0 NROrb= 390 NOA= 26 NOB= 26 NVA= 364 NVB= 364 **** Warning!!: The largest alpha MO coefficient is 0.15708377D+03 Leave Link 801 at Tue Nov 6 22:58:30 2001, MaxMem= 65536000 cpu: 0.0 (Enter /user/lokal/ga98/l906.exe) Frozen-core derivative calculation, NFC= 10 NFV= 0. FulOut=F Deriv=T AODrv=F MMem= 1 MDisk= 26 MDiskD= 26 W3Min= 5760000 MinDsk= 7184600 NBas6D= 400 NBas2D= 80668 NTT= 80200 LenExt= 63070460 MDV= 65070460 MDiskM= 2189 NBas2p= 72052 Disk-based method using ON**2 memory for 26 occupieds at a time. Estimated scratch disk usage= -1 words. IMap= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 IMap= 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 Inconsistency from DE2Siz in DoE2D. Error termination via Lnk1e in /user/lokal/ga98/l906.exe. Job cpu time: 0 days 3 hours 34 minutes 30.4 seconds. File lengths (MBytes): RWF= 78 Int= 0 D2E= 0 Chk= 3 Scr= 1 ------------------------------------------------------------------------------------------------------------------------------------------------------------- Is it a problem of disk space? The rwf files are defined as %rwf=f1,4000MB,f2,4000MB,f3,2000MB Your kind assistance will be highly appreciated. Thanks -- Gustavo Velardez. PhD in Chemistry gust@fisquim.fcq.unc.edu.ar INFIQC. Departamento de Fisicoquimica. Universidad Nacional de Cordoba. ARGENTINA From chemistry-request@server.ccl.net Wed Nov 7 07:34:54 2001 Received: from mailserver.unimi.it ([159.149.10.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7CYsB10606 for ; Wed, 7 Nov 2001 07:34:54 -0500 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id NAA04970 for ; Wed, 7 Nov 2001 13:34:53 +0100 (MET) Message-ID: <024101c16788$72757cc0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "CCL" Subject: Announcing VEGA1.3.2 Date: Wed, 7 Nov 2001 13:33:47 +0100 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCLers, we are glad to announce that the final 1.3.2 release of VEGA package (AmigaOS, Irix, Linux and Win32) is now ready for free download on our web server (http://users.unimi.it/~ddl). New in this release: - Now VEGA can read the DCD files in little or big endian format without conversion. - Added the PDB ATDL (PDBA) file support (read and write). - Fix: Fasta saver. - Win32: more mouse controls trough the middle button and the wheel. - Win32: added Select menu item to show/hide a part of a molecule. - Win32: added Color -> By residue, Color -> By chain and Color -> By charge menu item. - Win32: new Save Image output formats (Gif, Jpeg, OpenIL, PCX, PNG, PNM, Raw, SGI, Targa and Tiff). - Win32: added the View Settings dialog box. - Win32: improved CPK visualization. - Win32: added VdW Dotted and Liquorice visualization modes. - Win32: some configuration parameters (window size and position, menu checkmarks, etc) are stored when the program is closed. - Win32: menu history of the opened files. - Win32: added window popup menu to resize the main. - Win32: more than one VEGA session can be opened at the same time. - Win32: drag & drop function to open the molecules. - SendVegaCmd can control more than one VEGA session. - SendVegaCmd asyncronous mode. Thank you for your attention. Giulio Vistoli & Alessandro Pedretti -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-58357522 Fax +39-02-58357565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Wed Nov 7 05:04:49 2001 Received: from shardagate.mahindrabt.com ([206.102.1.162]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7A4lB08740 for ; Wed, 7 Nov 2001 05:04:48 -0500 Received: from mahindrabt.com (mailscan.sharda.mahindrabt.com [10.5.0.97]) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) with ESMTP id PAA21333 for ; Wed, 7 Nov 2001 15:34:40 +0530 X-SMTP-Sending-IP: 10.5.0.15 Received: from intranet.sharda.mahindrabt.com by mahindrabt.com ; 7 Nov 2001 14:31:07 +0000 Received: from mahindrabt.com ([10.5.2.39]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id PAA03033 for ; Wed, 7 Nov 2001 15:34:30 +0530 X-MSReally-To: chemistry@ccl.net Message-ID: <3BE9058F.43286A09@mahindrabt.com> Date: Wed, 07 Nov 2001 15:27:35 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PLSR scaling Content-Type: multipart/mixed; boundary="------------FB557E8C9A5AA2AC0C4C84CF" This is a multi-part message in MIME format. --------------FB557E8C9A5AA2AC0C4C84CF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have a questions for researchers in statistical analysis. What is the difference in Partial Least Squares Regression (PLSR) equation, when the subjected data is scaled or non-scaled? How does the scaling of data affect the PLSR equation? Any references, pointers or web pages explaining this clearly are highly appreciated. Thanks & regards. Sudhir ********************************************************* Disclaimer This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited. ********************************************************* Visit us at http://www.mahindrabt.com --------------FB557E8C9A5AA2AC0C4C84CF Content-Type: text/x-vcard; charset=us-ascii; name="sudhirk.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Sudhir A. Kulkarni Content-Disposition: attachment; filename="sudhirk.vcf" begin:vcard n:Kulkarni;Dr. Sudhir A. tel;fax:+91-20-542-4466 tel;work:+91-20-401-8350 x-mozilla-html:FALSE url:www.mahindrabt.com org:Mahindra British Telecom Limited;Research and Development version:2.1 email;internet:sudhirk@MahindraBT.com title:Consultant adr;quoted-printable:;;Sharda Center, Off Karve Road=0D=0AErandwane;Pune;Maharashtra;411 004;India x-mozilla-cpt:;32608 fn:Dr. Sudhir A. Kulkarni end:vcard --------------FB557E8C9A5AA2AC0C4C84CF-- From chemistry-request@server.ccl.net Wed Nov 7 10:10:31 2001 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7FAVB13182 for ; Wed, 7 Nov 2001 10:10:31 -0500 Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA24955; Wed, 7 Nov 2001 17:09:49 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Wed, 7 Nov 2001 17:09:49 +0200 (EET) From: Tom Sundius X-Sender: To: Armando Navarro cc: Subject: Re: CCL:complex exp(x2) integrals In-Reply-To: <000e01c166c6$0a43ae50$935290c1@usc.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 6 Nov 2001, Armando Navarro wrote: > Dear Members: > Can anybody point me to routines (or simply numerical algorithms) for solution of complex integrals of the form: > > int (exp(x2)dx) , with limits between 0 and z, being z a complex number >of the form a+bi. > The text in the paper says that this integral can be related to >complex error function, however I was not capable >to establish the relationship. The complex error function of Faddeyeva and Terent'ev is defined as w(z)=exp(-z^2)(1+(2i/sqrt(pi))*int_0^z (exp(t^2)dt)). It is also expressed as exp(-z^2)*erfc(-iz), where erfc is the complementary error function (erfc z = 1 - erf z). There is a chapter about the error function in the Handbook of Mathematical Tables by Abramowitz and Stegun. This chapter was written by Walter Gautschi, who also wrote an efficient algorithm to compute it to ten decimals (see SIAM J. Numer. Analysis 7, 187-198 (1970)). An even more efficient algorithm has been published by Poppe and Wijers (Fortran version in http://www.netlib.org/toms/680) The real part of the complex error function is related to the Voigt function (see, for instance, T. Sundius: J.Raman Spectrosc. 1, 471-488 (1973)). Greetings, TS Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 From chemistry-request@server.ccl.net Wed Nov 7 10:40:47 2001 Received: from chemistry.chem.utah.edu ([128.110.197.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7FekB13941 for ; Wed, 7 Nov 2001 10:40:46 -0500 Received: from ANDERSON5 (anderson5.chem.utah.edu [128.110.196.158]) by chemistry.chem.utah.edu (Switch-2.0.6/Switch-2.0.6) with SMTP id fA7FdUt00425; Wed, 7 Nov 2001 08:39:31 -0700 (MST) Message-ID: <030b01c167a2$6ae9bab0$9ec46e80@ANDERSON5> From: "Scott Anderson" To: "surface surface" , "MDN MDN" , Subject: Cluster Symposium Date: Wed, 7 Nov 2001 08:39:41 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Please excuse me if you get duplicates of this message. Dear Colleague: I am organizing a symposium on "The Chemical and Physical Properties of Supported and Isolated Metal Nanoclusters" for the Division of Chemical Physics of The American Physical Society. The symposium is an attempt to get together a wide selection of groups active in cluster deposition, cluster chemistry, cluster-based materials, and related areas. The format will include a contributed talks, and I encourage you to submit a contributed paper for oral presentation, if you are working in an area related to the topic. The symposium (APS calls it a special focus topic) will be at the annual March Meeting of The American Physical Society to be held March 18-22, 2002 in Indianapolis, IN in the Indiana State Convention Center. Complete abstract submission instructions can be found at the APS web site. http://www.aps.org/meet/MAR02/. The deadline for receipt of abstracts is 5:00 pm EST December 7, 2001. The topic number of the symposium is DCP Special Focus Topic 11.9.1 Invited Speakers: U. Heiz (U. Ulm), A. Nakajima (Keio U.), J. Murakami(AIST, Nagoya), C. Binns (U. Leicester), W. Harbich (Ecole Polytech. Lausanne), S. Anderson (U. Utah), D. W. Goodman (Texas A&M), M. Duncan (U. Georgia), T. Kondow (Toyota Tech.), J. Parks (Rowland Inst), U. Landman (Ga. Tech). Chemical and Physical Properties of Supported and Isolated Metal Nanoclusters (DCP) Supported metal nanoclusters are important in many catalysts and in other materials applications. It is known that the chemical and materials properties of supported clusters depend strongly on parameters such as cluster size, morphology, and oxidation state, and also on support properties such as defect structure and redox behavior, however, the origin of the effects is not understood. Recently, there have been major advances in the study of supported clusters using both deposition of size-selected clusters and controlled nucleation of clusters on supports. Simultaneously, new spectroscopic, diffraction, and imaging methods have been developed that allow detailed study of isolated clusters. This focus session will provide a forum for discussion and comparison of different approaches to probing the relationships between the physical, chemical, and materials properties of metal nanoclusters. Experimental and theoretical papers are solicited in any related area, including, but not limited to: Deposition of energy and/or mass-selected clusters, Growth, mobility, properties of cluster on surfaces. Physical and chemical properties of isolated (gas-phase) metal clusters. Nano-cluster-based catalysts or materials. Theory on clusters or cluster-support interactions. Prof. Scott L. Anderson Department of Chemistry University of Utah 315 S. 1400 E. Rm 1216 Salt Lake City, UT 84112 (801)585-7289 FAX(801)581-8433 www.chem.utah.edu/chemistry/faculty/anderson/anderson.html From chemistry-request@server.ccl.net Wed Nov 7 17:50:07 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7Mo7B22672 for ; Wed, 7 Nov 2001 17:50:07 -0500 Received: from minghu (exothermic-01.dynamic.rpi.edu [128.113.21.156]) by mail.rpi.edu (8.11.3/8.11.3) with SMTP id fA7Mo7P62346 for ; Wed, 7 Nov 2001 17:50:07 -0500 Message-ID: <003601c167de$53ba3f40$9c157180@dynamic.rpi.edu> From: "Jerry Song" To: "CCL" References: <3BDD5E91.CB1490D2@lctn.uhp-nancy.fr> Subject: similarity of 3D property-mapped-surface Date: Wed, 7 Nov 2001 17:48:32 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hello, Are there ant references about the comparison of similarity of property-encode-surfaces? Thanks, From chemistry-request@server.ccl.net Wed Nov 7 17:10:30 2001 Received: from gateway.bioreason.com ([207.108.245.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7MAUB21866 for ; Wed, 7 Nov 2001 17:10:30 -0500 Received: by gateway.bioreason.com (Postfix, from userid 200) id 9650B759; Wed, 7 Nov 2001 16:32:25 -0700 (MST) Received: by bioreason.com via smwrap Version 1.0 id smwrapUhO30a; Wed Nov 7 16:31:34 2001 by mailhost.bioreason.com (Postfix) with ESMTP id 32DE03894; Wed, 7 Nov 2001 16:19:11 -0700 (MST) Message-ID: <3BE9B263.E3549CEC@bioreason.com> Date: Wed, 07 Nov 2001 15:14:59 -0700 From: Organization: Bioreason MIME-Version: 1.0 To: Cc: Jan Labanowski Subject: Bioreason's ClassPharmer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Subscribers, Bioreason has just released ClassPharmer, the first module of a new software system for automating analysis of data from screening libraries of compounds. ClassPharmer provides topologically relevant structural classification, placing compounds into classes based on large, significant scaffolds that are learned on the fly. The science underneath includes knowledge-based reasoning and a new MCS algorithm that makes use of the Bioreason's topological key technology. Some of the issues we had in mind when we created it might be of interest to you, such as... o QSAR analysis works well only when you have a reasonably homogeneous set of compounds on which to begin the analysis. o With the noisy results from HTS or computational docking, the class characteristics are really more relevant than any particular compound readout. o With a diverse set of compounds reporting positive in an assay, classes frequently have naturally overlapping memberships, depending on the scaffold defining the class. Feel free to download it and take a look at www.bioreason.com. Thanks. --Susan Susan I. Bassett, Ph.D. Bioreason, Inc. info@bioreason.com From chemistry-request@server.ccl.net Wed Nov 7 13:08:15 2001 Received: from pesto.q1.fcen.uba.ar ([157.92.31.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7I88B16828 for ; Wed, 7 Nov 2001 13:08:10 -0500 Received: from localhost (alec@localhost) by pesto.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id PAA02084 for ; Wed, 7 Nov 2001 15:05:00 -0300 Date: Wed, 7 Nov 2001 15:05:00 -0300 (ART) From: Alejandro Crespo To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sirs: I'm trying to make a geometry optimization using a solvation model, the principal problem is that in the manual the use of the PCM approach is recomended only for SP calculations. Also it said that for geometry optimizations the recomended method is SCIPCM, but I have problems of no convergence with the default parameters. I will apreciated any suggestion regarding this issue. Thank you very much. Alejandro Crespo From chemistry-request@server.ccl.net Wed Nov 7 14:37:38 2001 Received: from cecalc.ula.ve ([150.185.138.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA7JZAB18212 for ; Wed, 7 Nov 2001 14:35:49 -0500 Received: from cecalc.ula.ve (eolos.cecalc.ula.ve [150.185.138.22]) by cecalc.ula.ve (8.9.3/8.9.3) with ESMTP id OAA13184; Wed, 7 Nov 2001 14:39:57 -0400 Sender: risea@cecalc.ula.ve Message-ID: <3BE98691.6B906E3D@cecalc.ula.ve> Date: Wed, 07 Nov 2001 15:08:01 -0400 From: Raul Isea X-Mailer: Mozilla 4.61 [en] (X11; I; AIX 4.2) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Grid Computing in Merida, Venezuela!! References: <3BE90A34.7202682F@argon.ch.ic.ac.uk> Content-Type: multipart/alternative; boundary="------------DAB2227F1AA64BF4A02F5FFE" --------------DAB2227F1AA64BF4A02F5FFE Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers Please excuse me if you get duplicates of this message. The Center for Scientific Research of Universidad de Los Andes (CeCalCULA, http://www.cecalc.ula.ve) announces the Second Latin-American Course on Parallel and High Performance Computing, to be held in Mérida, Venezuela, from December 3 to 7, 2001. This course is aimed to undergraduated, postdoctoral, Ph.D. students and junior research faculty working in computational areas related to Chemistry, Physics, Mathematics, Biology, surface science, catalysis and other related sciences. Participants are expected to have basic theoretical knowledge on computational sciences. This year, Grid Computing, a novel paradigm aiming to exploit a large number of resources geographically distributed through the Internet, will be the main focus of the course. Professors: John Boisseau - Texas Advanced Computing Center, USA Jack Dongarra - University of Tennessee & Oak Ridge National Lab, USA Barton Miller - University of Wisconsin Henry Casanova - University of California, USA Ben Segal - CERN, Switzerland. Antonio Redondo - Los Alamos, USA Z. Hong Zhou - University of Texas - Health Science Center, USA Gustavo Scuseria - Rice University, USA Reinaldo Pis Diez - La Plata, Argentina Victor Pereyra - Weidlinger Associates, USA José Castillo - San Diego State University, USA Gerardo Cisneros - SGI, Mexico Registration The registration fee, US$300, covers lecture notes and social events. More information can be found at http://www.cecalc.ula.ve/elpcar2/planilla00.html Scholarships A reduced number of scholarships covering the registration fee will be available. Overseas participants are encouraged to apply. Applications should include a curriculum vitae and a letter of recommendation written by the supervisor. Exhibits Booths are available to sponsors of this event. Companies offering services and/or products related to high performance computing, distributed computing, database integration, bioinformatics, and other technologies, that could benefit from exhibiting, are encouraged to contact us at elpcar2@cecalc.ula.ve. Posters Poster presentations will be chosen from abstracts received and approved. Each participant is encouraged to submit one abstract. You MUST submit your abstract by E-mail (elpcar2@cecalc.ula.ve). For further information please send your inquiries to elpcar2@cecalc.ula.ve or http://www.cecalc.ula.ve/elpcar2/abstracts.html Deadlines - Application form: October 30th 2001 Notification: November 5th 2001 Registration Fee Payment: October 30th 2001 Poster submission: October 30th 2001 Sponsors FONACIT FUNDACITE-Mérida SUN de VENEZUELA SILICON GRAPHICS de VENEZUELA Additional information can be found at the Course's web site, at http://www.cecalc.ula.ve/elpcar2/ -- Dr. Raul Isea Ph. D. in Chemistry Email: risea@cecalc.ula.ve; lrisea@yahoo.com http://www.cecalc.ula.ve/~risea --------------DAB2227F1AA64BF4A02F5FFE Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear  CCLers
Please excuse me if you get duplicates of this message.

The Center for Scientific Research of Universidad de Los Andes
(CeCalCULA, http://www.cecalc.ula.ve) announces the
Second Latin-American Course on Parallel and High Performance Computing,
to be held in Mérida, Venezuela, from December 3 to 7, 2001.

This course is aimed to undergraduated, postdoctoral, Ph.D. students and junior research
faculty working in computational areas related to Chemistry, Physics, Mathematics, Biology,
surface science, catalysis and other related sciences.  Participants are expected to have
basic theoretical knowledge on computational sciences.  This year,  Grid Computing,
a novel paradigm aiming to exploit a large number of resources
geographically distributed through the Internet, will be the main focus of the course.

Professors:
John Boisseau - Texas Advanced Computing Center, USA
Jack Dongarra - University of Tennessee & Oak Ridge National Lab, USA
Barton Miller - University of Wisconsin
Henry Casanova - University of California, USA
Ben Segal - CERN, Switzerland.
Antonio Redondo - Los Alamos, USA
Z. Hong Zhou - University of Texas - Health Science Center, USA
Gustavo Scuseria - Rice University, USA
Reinaldo Pis Diez - La Plata, Argentina
Victor Pereyra - Weidlinger Associates, USA
José Castillo - San Diego State University, USA
Gerardo Cisneros - SGI, Mexico

Registration
The registration fee, US$300, covers lecture notes and social events.  More information
can be found at http://www.cecalc.ula.ve/elpcar2/planilla00.html

Scholarships
A reduced number of scholarships covering the registration fee will be available. Overseas participants
are encouraged to apply.   Applications should include a curriculum vitae and a letter of recommendation
written by the supervisor.

Exhibits
Booths are available to sponsors of this event. Companies offering services and/or products related
to high performance computing, distributed computing, database integration, bioinformatics,
and other technologies, that could benefit from exhibiting, are encouraged to contact us
at elpcar2@cecalc.ula.ve.

Posters
Poster presentations will be chosen from abstracts received and approved.   Each participant
is encouraged to submit one abstract. You MUST submit your abstract by E-mail
(elpcar2@cecalc.ula.ve).   For further information please send your
inquiries to elpcar2@cecalc.ula.ve or http://www.cecalc.ula.ve/elpcar2/abstracts.html

Deadlines - Application form: October 30th 2001
Notification: November 5th 2001
Registration Fee Payment: October 30th 2001
Poster submission: October 30th 2001

Sponsors
FONACIT
FUNDACITE-Mérida
SUN de VENEZUELA
SILICON GRAPHICS de VENEZUELA

Additional information can be found at the
Course's web site, at http://www.cecalc.ula.ve/elpcar2/
  

-- 
Dr. Raul Isea
Ph. D. in Chemistry
Email: risea@cecalc.ula.ve;  lrisea@yahoo.com
http://www.cecalc.ula.ve/~risea
  --------------DAB2227F1AA64BF4A02F5FFE--