From chemistry-request@server.ccl.net Thu Aug 31 16:42:07 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA06010 for ; Thu, 31 Aug 2000 16:42:06 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id WAA16456; Thu, 31 Aug 2000 22:42:22 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14766.49964.527690.112403@yogi.pc1.uni-duesseldorf.de> Date: Thu, 31 Aug 2000 22:42:20 +0200 (CEST) From: Jochen Kuepper To: Krzysztof Radacki Cc: Alexander Hofmann , chemistry@ccl.net Subject: CCL:Linux settings to run in parallel In-Reply-To: <001701c01362$c238d0c0$d43b8286@dorf.rwthaachen.de> References: <001701c01362$c238d0c0$d43b8286@dorf.rwthaachen.de> X-Mailer: VM 6.72 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id QAA06011 Krzysztof Radacki writes: > Just edit it with vi or whatever editor you like. Only one small problem is > that after each restart it has old value. So what I did was adding to some > script the line echo "400000000" > /proc/sys/kernel/shmmax (I belive that it > was /etc/profile but unfortunately my linux computer is not available for me > in next two weeks, so i can't proof it). /etc/rc.d/rc.local would do the job, I guess;-)) Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195 From chemistry-request@server.ccl.net Thu Aug 31 17:30:18 2000 Received: from sirocco.cc.mcgill.ca (sirocco.CC.McGill.CA [132.206.27.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06199 for ; Thu, 31 Aug 2000 17:30:18 -0400 Received: from ariya430 (ariya430.Chem.McGill.CA [132.206.175.28]) by sirocco.cc.mcgill.ca (8.9.1/8.9.1) with SMTP id RAA03616 for ; Thu, 31 Aug 2000 17:30:18 -0400 (EDT) Message-Id: <200008312130.RAA03616@sirocco.cc.mcgill.ca> From: "Alexei Khalizov" Organization: Chemistry Dept., McGill University To: chemistry@ccl.net Date: Thu, 31 Aug 2000 17:30:20 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: SUMMARY and A PROBLEM: QCISD()/CCSD() and T1Diag Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id RAA06200 Hello and thank you for all of your responses, This is a summary on my question about using the QCISD and CCSD keywords. The problem was in the duplication of the method keyword. The correct route command looks alike # QCISD(MaxCycle=40,T1Diag)/6-31G* Alas, I wasn't able to perform T1Diag even using correct keywords. At one of the CCSD/QCISD iterations I have got a Windows' message that program (link L913) performed an illegal operation ... I tried both QCISD(T1Diag) and CCSD(T1Diag) for different molecules (closed- and open shell) and with various basis sets - no changes. I asked my friend to try the same calculations with an older version of G98w - he has got the same result. P.S. T1Diag DOES work if I don't specify basis set (STO-3G is used as a default). It also works with STO-3G* basis set. Strange!? ------------------------------------------ > Yeah, I've heard that funny things can happen if you repeat a > correlation-method keyword. You can write: > QCISD(maxcyc=40) 6-31G* > and this should give you the calc. you want. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Any opinions herein are not necessarily representative of > Süd Chemie. ------------------------------------------- > Dr. Alexei Khalizov, > > G98/G98W can calculate the T1/Q1 diagnostic. For the Q1 diagnostic: > > #P QCISD(T1Diag) > > and for the T1 diagnostic: > > #P CCSD(T1Diag) > > > (i) I found that upon any modifications applied with QCISD/CCSD > > keywords, e.g.: > > > > #P QCISD/6-31G* QCISD(MaxCycle=40) > > or > > #P QCISD/6-31G* QCISD(T1Diag) > > The problem above is the duplication of the method keyword (i.e. #p QCISD > QCISD). > > Sincerely, > > Gary W. Trucks -------------------------------------------- > Dear Alexei > You have a syntax error in your route > You must write > > #P QCISD(MaxCycle=40)/6-31G* > > However, I never succeded into run the T1Diag in Gaussian, if you are able > to do such calculation please let me know > > Armando Navarro > Departamento de quimica Organica > Facultade de quimica. Universidade de Santiago de Compostela > e-mail: qoajnv@usc.es ----------------------------------------------- > > Dr. Khalizov, > > As with other keywords in G98 you cannot repeat them on the > route so you should have > > # QCISD(MaxCycle=40,T1Diag)/6-31G* > > with any relevant options grouped with their associated keywords. > > The T1Diag will be computed and printed if you select it. As > you have not actually gotten into a method where T1Diag is relevant > try again with the above input and see if that does not resolve > your concern. > ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Fri Sep 1 10:12:32 2000 Received: from shardagate.mahindrabt.com (root@[206.102.1.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10787 for ; Fri, 1 Sep 2000 10:12:30 -0400 Received: (from uucp@localhost) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) id TAA11924 for ; Fri, 1 Sep 2000 19:42:09 +0530 Received: from UNKNOWN(10.5.0.15), claiming to be "intranet.sharda.mahindrabt.com" via SMTP by shardagate, id smtpdOJuU2k; Fri Sep 1 19:42:00 2000 Received: from mahindrabt.com ([10.5.2.73]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id TAA05546 for ; Fri, 1 Sep 2000 19:42:02 +0530 Message-ID: <39AFB74E.9AA5B1D4@mahindrabt.com> Date: Fri, 01 Sep 2000 19:33:59 +0530 From: vijay pargaonkar X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: "CHEMISTRY@ccl.net" Subject: ONLINE FACILITY FOR COMPUTATIONAL CHEMISTS X-Priority: 1 (Highest) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SUBJECT :- ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY Dear computational chemists and computational engineers, Now, you can make use of a common platform for online discussions on computational chemistry field. Just go to site http://www.science.domainvalet.com click on ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY. Regards, Pargaonkar Vijay C. From chemistry-request@server.ccl.net Fri Sep 1 10:03:11 2000 Received: from balder.nilu.no (balder.nilu.no [128.39.104.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10758 for ; Fri, 1 Sep 2000 10:03:10 -0400 Received: from afrodite.no. (afrodite.nilu.no) by balder.nilu.no (Sun Internet Mail Server sims.3.5.2000.01.05.12.18.p9) with ESMTP id <0G070091FOCWMS@balder.nilu.no> for chemistry@ccl.net; Fri, 1 Sep 2000 16:02:56 +0200 (MET DST) Received: from eshpc (eshpc.nilu.no. [128.39.66.15]) by afrodite.no. (8.9.1b+Sun/8.9.1) with SMTP id QAA19772 for ; Fri, 01 Sep 2000 16:02:58 +0200 (MET DST) Date: Fri, 01 Sep 2000 16:02:31 +0200 From: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Subject: Autodock- atom types To: CCL Reply-to: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Message-id: <006201c0141d$45f587e0$0f422780@nilu.no> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Priority: 3 Can Autodock handle Chlorine substituents in the ligand? It seems like Cl is read as C by 'mkgpf3'. Thanks in advance, ######################################### Eldbjørg S. Heimstad NILU Norwegian Institute for Air Research The Polar Environmental Centre N-9296 Tromsø, Norway Tel. +47-77 75 03 75 Fax. +47-77 75 03 76 E-mail: Eldbjorg.Sofie.Heimstad@nilu.no Web: http://www.nilu.no ######################################### From chemistry-request@server.ccl.net Fri Sep 1 10:44:38 2000 Received: from mailhub2.shef.ac.uk (mailhub2.shef.ac.uk [143.167.2.154]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10946 for ; Fri, 1 Sep 2000 10:44:38 -0400 Received: from stoat.shef.ac.uk ([143.167.2.1]) by mailhub2.shef.ac.uk with esmtp (Exim 3.02 #2) id 13Us3N-0005vK-00 for chemistry@ccl.net; Fri, 01 Sep 2000 15:44:25 +0100 Received: from li1vg (helo=localhost) by stoat.shef.ac.uk with local-esmtp (Exim 3.14 #2) id 13Us3N-0002TR-00 for chemistry@ccl.net; Fri, 01 Sep 2000 15:44:25 +0100 Date: Fri, 1 Sep 2000 15:44:25 +0100 (BST) From: Val Gillet X-Sender: li1vg@stoat To: chemistry@ccl.net Subject: Sheffield 2001: REMINDER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII *************************** REMINDER ***************************** DEADLINE FOR CALL FOR PAPERS 15th SEPTEMBER 2000 ***************************************************************** The Chemical Structure Association and the Molecular Graphics and Modelling Society announce their Second Joint Sheffield Conference on Chemoinformatics: Computational Tools for Lead Discovery. The conference will be held in Stephenson Hall, University of Sheffield, UK from 9th to 11th April 2001. Offers of papers are welcomed in all aspects of lead discovery. Possible topics include (but are not limited to): * 3D databases, including docking and pharmacophore analysis; * assay QC and its influence on data mining; * chemical data mining; * descriptor validation; * design of leadlike combinatorial libraries; * design of screening collections; * e-business to facilitate lead discovery; * novel software and hardware systems for lead discovery; * selective compound acquisition from in house and commercial suppliers; * similarity and clustering methods; * structure-activity methods for lead identification and early optimisation; * structure-based design for lead identification and early optimisation; * virtual screening; * case histories incorporating any of the above. Authors interested in submitting a paper for consideration should send a title and brief abstract to Val Gillet (v.gillet@sheffield.ac.uk) by 15th September 2000. Further details of the conference are posted at http://cisrg.shef.ac.uk/shef2001 From chemistry-request@server.ccl.net Fri Sep 1 14:50:23 2000 Received: from cheviot3.ncl.ac.uk (root@cheviot.ncl.ac.uk [128.240.233.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA12061 for ; Fri, 1 Sep 2000 14:50:22 -0400 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot3.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id e81IoN721102 for ; Fri, 1 Sep 2000 19:50:23 +0100 (BST) Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id TAA05833 for ; Fri, 1 Sep 2000 19:50:23 +0100 (BST) X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Fri, 1 Sep 2000 19:50:23 +0100 (GMT) From: "Bruce. Tattershall" To: Computational Chemistry List Subject: DFT geometry oscillating non-convergence Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.8 (cheviot3) I am calculating geometries for fairly large (7 P,S; 32 C,N; 24 H; no symmetry) polycyclic molecules, with a view to calculating phosphorus NMR shieldings. Using g94, the geometry optimisations eventually converged at the RHF/3-21G* level, and RHF/GIAO calculations using these geometries are fairly encouraging in respect of fitting differences in observed chemical shifts. Conformations seem to be controlled by non-bonded interactions between hydrogens on saturated carbons of 1,2,3,4-tetrahydroisoquinolide substituents, and the phosphorus sulfide cage. To do better than this, I need better geometries. In g98 I am now trying MPWPW91 or MPW1PW91 DFT optimisations, using Ahlrichs SV basis with single d polarisation functions on N, P and S, but not on C or H. (I am using the MPWPW91 rather than BLYP functionals because work elsewhere seems to show that they give better geometries for heavy main-groups polcyclics. The Ahlrichs SV basis works well for RHF geometries on polyphosphorus polycyclics, and can readily be followed by his TZV basis for sp calculations.) Using either DFT method, starting from the RHF/3-21G* geometry, the geometry fails to converge to the default g98 limits. Energy and forces go down nicely for the first twelve geometry points, but before that, when the forces are already well within the g98 convergence limits, the geometry starts making large displacement jumps. After 16 points, energy stops converging and starts to oscillate, along with forces and displacements. The optimisation seems to be in a bumpy very flat-bottomed minimum which g98 seems unable to settle into the bottom of. Visually (using molden) one can correspondingly see the geometry oscillating between what look like fairly well repeated conformations. The coordinates which give the big displacements are dihedral angles defining the conformation of the saturated part of the isoquinolide bicycle. The tendency of this to settle to a particular conformation seems to be interfered with by its non-bonded interactions with the PS cage. At the MPWPW91 level, I tried starting a fresh opt run, inputting coordinates from one of the best points so far, to see whether g98 could be jogged into setting off in a slightly more successful direction, but this had a similar result. I know I can use opt=loose in g98, but will this help me to get a good enough geometry? Please can someone advise? I am sorry if this is all old news in CCL, but as a newcomer I failed to find anything clearly useful in several hours of dredging through the archive using the search terms I thought of. Many thanks, Bruce Tattershall Department of Chemistry, Univ. of Newcastle, England. email: Bruce.Tattershall@newcastle.ac.uk From chemistry-request@server.ccl.net Fri Sep 1 16:25:12 2000 Received: from sirocco.cc.mcgill.ca (sirocco.CC.McGill.CA [132.206.27.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12400 for ; Fri, 1 Sep 2000 16:25:12 -0400 Received: from ariya430 (ariya430.Chem.McGill.CA [132.206.175.28]) by sirocco.cc.mcgill.ca (8.9.1/8.9.1) with SMTP id QAA14925; Fri, 1 Sep 2000 16:25:06 -0400 (EDT) Message-Id: <200009012025.QAA14925@sirocco.cc.mcgill.ca> From: "Alexei Khalizov" Organization: Chemistry Dept., McGill University To: Bruce.Tattershall@newcastle.ac.uk Date: Fri, 1 Sep 2000 16:25:20 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:DFT geometry oscillating non-convergence CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Hello Bruce, You may try Opt(NRScale) or Opt(NRScale, Newton) keywords, which request that if the step size in the Newton-Raphson step exceeds the maximum, then it will be scaled back. Opt(NoNRScale, RFO) is default for non-TS geometry optimization. Regards ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Fri Sep 1 20:48:31 2000 Received: from chem_mail.chem.sc.edu (mail.chem.sc.edu [129.252.75.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA13295 for ; Fri, 1 Sep 2000 20:48:30 -0400 Received: from MOLETRONICS ([129.252.38.205]) by chem_mail.chem.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id Q9Z6H38T; Fri, 1 Sep 2000 20:48:23 -0400 Message-ID: <006901c01477$94d93320$cd26fc81@psc.sc.edu> Reply-To: "derosa" From: "derosa" To: Subject: MM/MD programs Date: Fri, 1 Sep 2000 20:48:59 -0400 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all, Can someone help me to find out a versatile MM/MD program (freeware or not), where the force field equations can be changed or added at will. Certainly, the availability of the source code is imperative. I will summarize your answers. Thanks ********************************** Dr. Pedro Derosa Dept of Chemistry and Biochemistry University of South carolina Ph. (803) 777-8401 Fax (803) 777-9521 **********************************