From chemistry-request@server.ccl.net Fri Jun 18 04:58:00 1999 Received: from nic.upatras.gr (nic.upatras.gr [150.140.1.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA05671 for ; Fri, 18 Jun 1999 04:57:58 -0400 Received: (qmail 8506 invoked from network); 18 Jun 1999 08:49:38 -0000 Received: from titanas.chemistry.upatras.gr (150.140.180.134) by nic.upatras.gr with SMTP; 18 Jun 1999 08:49:38 -0000 Received: (qmail 13900 invoked from network); 18 Jun 1999 08:30:08 -0000 Received: from rea.chemistry.upatras.gr (HELO titanas.chemistry.upatras.gr) (150.140.180.157) by titanas.chemistry.upatras.gr with SMTP; 18 Jun 1999 08:30:08 -0000 Message-ID: <376A0CA3.3C694420@titanas.chemistry.upatras.gr> Date: Fri, 18 Jun 1999 12:08:52 +0300 From: Demetrios Xenides X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: G94-Linux, ***missing separator???!!! Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Dear Collegues, I have posted a message some days ago and all the answers i got were quite helpfull. They will be posted in a day or two. However I would like most thank Marc C. Nicklaus for his precious help. It seems that the whole effort will be much more complicated than at first thought. So I tried oncemore (actually much much more)to built G94 but this time I got the following message. ../bsd/g94.make:103:*** missing separator. Stop As i understand in line 103 has a problem called "missing separator". Any help is very much wellcome Cheers Demetrios From chemistry-request@server.ccl.net Fri Jun 18 06:07:46 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA06168 for ; Fri, 18 Jun 1999 06:07:42 -0400 Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JCJMLOM0BA00027V@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Fri, 18 Jun 1999 11:59:12 +0200 Date: Fri, 18 Jun 1999 11:58:26 +0200 From: Krzysztof Radacki Subject: isosurface Sender: root@mail.rwth-aachen.de To: CCL Message-id: <376A1842.F8D8FD3@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi CCL'ers Can somebody sugest me free or working-demo program that can plot 3d-isosurfaces from discrete data (not just functions)? The best would be if I could choose value of F(x,y,z) that I want to plot. It can be for one of systems like: Linux, Windoof or Aix. regards Krzys Radacki _________________------------------------------------------------ ----------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Jun 18 07:09:34 1999 Received: from neon.ch.pwr.wroc.pl (neon.ch.pwr.wroc.pl [156.17.2.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06703 for ; Fri, 18 Jun 1999 07:09:27 -0400 Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id NAA03099 for ; Fri, 18 Jun 1999 13:03:57 +0200 (MDT) Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <376A279C.41C6@neon.ch.pwr.wroc.pl> Date: Fri, 18 Jun 1999 13:03:56 +0200 From: Jolanta Grembecka Organization: Wroclaw University of Technology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: MP2 calculations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's I have a problem with MP2 calculations for a system (dimer) which contains HCOO- and phosphonic analogue of leucine (LeuP). I have calculated MP2 energy for whole dimer as well as for LeuP in dimer basis set, but there are some problems with such calculations for HCOO- in dimer basis set. There is a fragment of output file: ------------ SCF Done: E(RHF) = -188.175925036 A.U. after 14 cycles Convg = 0.6171D-08 -V/T = 1.9994 S**2 = 0.0000 Range of M.O.s used for correlation: 4 247 NBasis= 247 NAE= 12 NBE= 12 NFC= 3 NFV= 0 NROrb= 244 NOA= 9 NOB= 9 NVA= 235 NVB= 235 **** Warning!!: The largest alpha MO coefficient is 0.16960943D+02 Fully direct method using O(OVN) memory. JobTyp=1 Pass 1: I= 1 to 9. PickT4: no shell combinations can fit! NKLS2p= 560 NKLS2= 560 MaxCom= 499 Error termination via Lnk1e in /usr/prog/g98/l906.exe. ---------------- How to resolve this problem? Best regards Jola Grembecka Institute of Organic Chemistry Biochemistry and Biotechnology Wroclaw University of Technology From chemistry-request@server.ccl.net Fri Jun 18 08:02:41 1999 Received: from ac16.uni-paderborn.de (ac16.uni-paderborn.de [131.234.240.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA07186 for ; Fri, 18 Jun 1999 08:02:35 -0400 Received: from odin.walhalla.edu ([131.234.134.87]) by ac16.uni-paderborn.de (Netscape Messaging Server 3.5) with ESMTP id 253; Fri, 18 Jun 1999 13:37:17 +0200 Received: from mephisto (mephisto.walhalla.edu [192.168.14.11]) by odin.walhalla.edu (8.9.3/8.8.7) with SMTP id NAA02669; Fri, 18 Jun 1999 13:32:52 +0200 Message-Id: <199906181132.NAA02669@odin.walhalla.edu> X-Sender: grobie@192.168.14.254 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Demo Date: Fri, 18 Jun 1999 13:33:01 +0200 To: Krzysztof Radacki , CCL From: Thorsten Klein Subject: Re: CCL:isosurface In-Reply-To: <376A1842.F8D8FD3@ac.rwth-aachen.de> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" hi Krzysztof, >Can somebody sugest me free or working-demo program that can plot >3d-isosurfaces from discrete data (not just functions)? The best >would be if I could choose value of F(x,y,z) that I want to plot. I think that gnuplot 3.7 is able to fit for this task. it is a lot of command-line working, but it generates very nice graphs and has a great data-parsing ability. http://ntfreeware.zdv.uni-tuebingen.de/NTSOFT/UG010017.htm#364 as a possible starting point. > >It can be for one of systems like: Linux, Windoof or Aix. > you can at least have linux and windoof. hope that this helps you. thorsten From chemistry-request@server.ccl.net Fri Jun 18 10:24:23 1999 Received: from dulcinea.alcala.es (dulcinea.alcala.es [130.206.82.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08897 for ; Fri, 18 Jun 1999 10:24:16 -0400 Received: from uni.alcala.es ([172.30.21.144]) by dulcinea.alcala.es (8.9.1/8.9.1) with ESMTP id QAA27003 for ; Fri, 18 Jun 1999 16:13:26 +0200 (MET DST) Sender: morreale@dulcinea.alcala.es Message-ID: <376AD2CD.6A05599F@uni.alcala.es> Date: Fri, 18 Jun 1999 16:14:21 -0700 From: antonio morreale Organization: Universidad de Alcala de Henares X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: SCI-PCM bibliography Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, Does any body knows some recent publications about SCI-PCM method? Best wishes, Antonio Morreale P. D. My new mail adrress is antonio.morreale@uni.alcala.es, How I should update this new adrress in the CCL list? Thanks. From chemistry-request@server.ccl.net Fri Jun 18 07:38:12 1999 Received: from popcsi.unian.it (root@popcsi.unian.it [193.205.128.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06991 for ; Fri, 18 Jun 1999 07:38:10 -0400 Received: from anvax1.unian.it ([193.205.128.181]) by popcsi.unian.it (8.8.7/8.8.7) with SMTP id NAA24213 for ; Fri, 18 Jun 1999 13:21:18 +0200 Message-Id: <3.0.32.19990618133337.007b3e50@popcsi.unian.it> X-Sender: roberta@popcsi.unian.it X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 18 Jun 1999 13:33:41 +0200 To: CHEMISTRY@ccl.net From: Roberta Galeazzi Subject: AM1 and LUMOs 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 HAA06992 Dear CCLs, could anyone give some references about the reliability of the AM1 method in calculating both shape and energy of LUMOs? Thanks in advance to all of you. I will summarize the answers Roberta **************************************************************************** ******* Dr. Roberta Galeazzi Università di Ancona Dipartimento di Scienze dei Materiali e della Terra via Brecce Bianche I-60131 Ancona ITALY tel.: +39-71-2204707 fax: +39-71-2204714 e-mail: roberta@popcsi.unian.it From chemistry-request@server.ccl.net Fri Jun 18 07:54:01 1999 Received: from sg1503.chemie.uni-marburg.de (root@sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA07103 for ; Fri, 18 Jun 1999 07:53:52 -0400 Received: from pc15105 (pc15105.Chemie.Uni-Marburg.DE [137.248.151.180]) by sg1503.chemie.uni-marburg.de (8.9.3/8.9.2/schn) with SMTP id NAA15037; Fri, 18 Jun 1999 13:44:52 +0200 (MEST) From: "Stefan Fau" To: "Jolanta Grembecka" Cc: "CCL" Subject: RE: MP2 calculations: PickT4 Date: Fri, 18 Jun 1999 13:49:05 +0200 Message-ID: <000301beb980$91523970$b497f889@pc15105.chemie.uni-marburg.de> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA07104 Dear Jolanta, the MP2 calculation dies because it does not find a working combination of something (maybe how to decide between RAM and disk usage). The calculation should run if you vary %mem or maxdisk a bit (up or down doesn't matter). Stefan ______________________________________________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Jolanta Grembecka > Sent: Friday, June 18, 1999 1:04 PM > To: chemistry@ccl.net > Subject: CCL:MP2 calculations > > > Dear CCL's > I have a problem with MP2 calculations for a system (dimer) which > contains HCOO- and phosphonic analogue of leucine (LeuP). I have > calculated MP2 energy for whole dimer as well as for LeuP in dimer basis > set, but there are some problems with such calculations for HCOO- in > dimer basis set. > There is a fragment of output file: > ------------ > SCF Done: E(RHF) = -188.175925036 A.U. after 14 cycles > Convg = 0.6171D-08 -V/T = 1.9994 > S**2 = 0.0000 > Range of M.O.s used for correlation: 4 247 > NBasis= 247 NAE= 12 NBE= 12 NFC= 3 NFV= 0 > NROrb= 244 NOA= 9 NOB= 9 NVA= 235 NVB= 235 > > **** Warning!!: The largest alpha MO coefficient is 0.16960943D+02 > > Fully direct method using O(OVN) memory. > JobTyp=1 Pass 1: I= 1 to 9. > PickT4: no shell combinations can fit! > NKLS2p= 560 NKLS2= 560 MaxCom= 499 > Error termination via Lnk1e in /usr/prog/g98/l906.exe. > ---------------- > > How to resolve this problem? > > Best regards > Jola Grembecka > Institute of Organic Chemistry Biochemistry and Biotechnology > Wroclaw University of Technology From chemistry-request@server.ccl.net Fri Jun 18 10:50:33 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA09271 for ; Fri, 18 Jun 1999 10:50:33 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id KAA20814 for ; Fri, 18 Jun 1999 10:42:11 -0400 (EDT) Received: from beckett.CERCA.UMontreal.CA (beckett.CERCA.UMontreal.CA [132.204.150.42]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id KAA12172 for ; Fri, 18 Jun 1999 10:42:11 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by beckett.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id KAA16124 for chemistry@ccl.net; Fri, 18 Jun 1999 10:42:10 -0400 (EDT) Message-Id: <199906181442.KAA16124@beckett.CERCA.UMontreal.CA> Subject: Database To: chemistry@ccl.net Date: Fri, 18 Jun 1999 10:42:10 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers, ------------ | Database | DOCK--> Known Enzyme | of all | Structure. | known drugs| ----------- I am looking for a database of all known drugs with their corresponding chemical structure and physical properties. Regards, Suzanne Sirois Ph.D. Chimie Computationnelle Office CERCA (Centre de Recherche en Calcul Applique) http://www.cerca.umontreal.ca/~siroiss e-mail: siroiss@cerca.umontreal.ca From chemistry-request@server.ccl.net Fri Jun 18 11:44:41 1999 Received: from argyle.richmond.edu (argyle.richmond.edu [141.166.97.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA10120 for ; Fri, 18 Jun 1999 11:44:38 -0400 Received: from configure (ur054083.richmond.edu [141.166.54.83]) by argyle.richmond.edu (8.9.0/8.9.0) with SMTP id LAA15972 for ; Fri, 18 Jun 1999 11:36:16 -0400 (EDT) Message-Id: <3.0.5.32.19990618113607.007e45d0@facstaff.richmond.edu> X-Sender: sabrash@facstaff.richmond.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 18 Jun 1999 11:36:07 -0400 To: CHEMISTRY@ccl.net From: "Samuel A. Abrash" Subject: CCl: G98 - Failure in initial guess Edited by CCL Cyber dog, jkl -- longer attachment placed on the Web as: http://www.ccl.net/cca/archived-messages/1999/06/18-appendix1.txt Dear CCl, We're setting up Gaussian 98 on a SGI R4400 machine. We ran the attached job, but ran into the problem that the initial guess for all MO's was zero. Can you help pinpoint what the problem with our setup is? The job runs ok (except for crashing when it fills up all available space on small (2Gbyte) hard drives when I run it on other machines. I'm sending the logfile for the job as an attachment. The attachment is: http://www.ccl.net/cca/archived-messages/1999/06/18-appendix1.txt Thanks for your assistance. Sam Abrash P.S. We're aware that help@gaussian.com is another option for this information, and have e-mailed them as well. --=====================_929734567==_ Content-Type: text/plain; charset="us-ascii" Sam Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu "The time it takes to complete a scientific project is given by the equation t = 2a + b where a is the original estimate, 2 is a correction factor, and b is a number large compared to 2a."