From chemistry-request@ccl.net Mon Aug 11 04:49:54 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7B8nr98013470 for >ccl.net>; Mon, 11 Aug 2003 04:49:53 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 19m8NS-0005tK-TR for chemistry<>ccl.net; Mon, 11 Aug 2003 09:50:06 +0100 Received: from matpc18.mats.qmw.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 19m8NR-0005QM-00 for chemistry<>ccl.net; Mon, 11 Aug 2003 09:50:05 +0100 Message-ID: <012a01c35fe5$45874bb0$402b258a@Ruzhen> From: "Ru-Zhen Li" >qmul.ac.uk> To: >ccl.net> Subject: question about BABEL Date: Mon, 11 Aug 2003 09:48:01 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Accept: This message was accepted by ls_accept.so The problem still exit, I put it in c:\BABELWIN and I put all the pdb files in the same directory, it didn't work there was only a DOS bat file generated, the content is: C:\BABELWIN>C:\ `C:\`is not recognized as an internal or external command, operable program or batch file. C:\BABELWIN>cd C:\BABELWIN C:\BABELWIN>babel -ip C:\BABELWIN\1N5U.PDB ox C:\BABELWIN\OUTPUT.XYZ but I cannot find the output.xyz file. PS: I downloaded the 32bit version, I do not know whether or not it is ok, because i do not know which version is proper for my computer but seems that neither 32 nor 16 works well. thanks! ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li<>qmul.ac.uk Materials Department Queen Mary University of London E1 4NS From chemistry-request@ccl.net Mon Aug 11 09:48:27 2003 Received: from vimg1.rdg.ac.uk (vimg1.rdg.ac.uk [134.225.1.81]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BDmR98026005 for ; Mon, 11 Aug 2003 09:48:27 -0400 Received: from vimp2.rdg.ac.uk ([134.225.16.91]) by vimg1 (Exim: gateway) with esmtp id 19mD2P-0002u0-00 for chemistry{at}ccl.net; Mon, 11 Aug 2003 14:48:41 +0100 Received: from vimh1.rdg.ac.uk ([134.225.16.83]) by vimp2.rdg.ac.uk (Exim: virusscanner) with esmtp id 19mD2J-0006xk-00 for chemistry{at}ccl.net; Mon, 11 Aug 2003 14:48:35 +0100 Received: from scpc12.rdg.ac.uk ([134.225.169.12]) by vimh1.rdg.ac.uk (Exim: host) with esmtp id 19mD2J-0001fj-00 for chemistry{at}ccl.net; Mon, 11 Aug 2003 14:48:35 +0100 Date: Mon, 11 Aug 2003 14:48:35 +0100 (BST) From: "M.T.Storr" X-X-Sender: marks@scpc12 To: CCL Subject: Re: CCL:g03 Error Message Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanner: exiscan *19mD2J-0006xk-00*SiUaHyiUJWA* (The University of Reading) Hi, in response to my question regarding the above-mentioned error, I thought that I would send some further details to clarify things. The calculation that I am attempting is being run upon an IBM SP3 and as such has been compiled as a set of 64 bit executables (I hope). The version we have is B.02 of Gaussian03. The input for the calculation is as follows: %Chk=X.chk %RWF=./1,8000MB,./2,8000MB,./3,8000MB,./4,8000MB,./5,8000MB,./6,8000MB %Mem=256MW # UHF/Gen SCF=(IntRep,Direct,MaxCycle=500,QC) Geom=(NoDistance,NoAngle) # Pseudo=Read PBC=(GammaOnly) and will crash before the error message if one does not allow 256MW. For reference the orginal erro message was: of initial guess= 2.0000 NB too large for integers on this machine. Error termination via Lnk1e in /prod/codes/castep/gaussian/g03/1508.exe at Any further suggestions would be gratefully received. Many thanks Mark From chemistry-request@ccl.net Mon Aug 11 13:49:33 2003 Received: from ns1.scripps.edu (ns1.scripps.edu [192.42.82.59]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BHnX98003372 for ; Mon, 11 Aug 2003 13:49:33 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id h7BHnkY00423 for ; Mon, 11 Aug 2003 10:49:46 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 20423; Mon, 11 Aug 2003 10:46:29 -0700 (PDT) Received: from renoir.scripps.edu (renoir [137.131.252.25]) by relay1.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id h7BHnBY28128; Mon, 11 Aug 2003 10:49:11 -0700 (PDT) Received: by renoir.scripps.edu (Postfix, from userid 1376) id 434E0DBB; Mon, 11 Aug 2003 10:49:11 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by renoir.scripps.edu (Postfix) with ESMTP id 31CBFD46; Mon, 11 Aug 2003 10:49:11 -0700 (PDT) Date: Mon, 11 Aug 2003 10:49:11 -0700 (PDT) From: Michael Crowley To: Rick Venable Cc: Michael Chen , Subject: Re: CCL:EWALD PME problem In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Rick, The transpose in CHARMM is a problem mainly because of the limitations in CHARMM's communication library. WIth full freedom to use simple MPI asynchronous send and receives, we could resolve a lot of the trouble. That remark is to justify the work I did to try to fix an abominable communication time during the FFT transpose (for the same basic algorithm CHARMM took 3-4 times as long as AMBER). Of the several methods I came up with, what appeared best was a binary-tree type idea which required a power-of-two number of PEs. THere is another method I worked out which only requires even number of PEs so there are always pairs communicating between each other. Anyway the bottom line is that the 2**N restriction will work the best, though an asychronous method is much better. You should try MPIFFT in your pref.dat and see if that gets you more of what you want. Yikes, I forgot all about these restrictions and making sure they got documented. Mike ----------------------------------------------------------------- Physical mail: Dr. Michael F. Crowley Department of Molecular Biology, TPC6 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037 Electronic mail: crowley-.at.-scripps.edu Telephone: 858/784-9290 Fax: 858/784-8688 ----------------------------------------------------------------- From chemistry-request@ccl.net Mon Aug 11 14:30:24 2003 Received: from mail-shield1.njit.edu (mail-shield1.njit.edu [128.235.251.171]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BIUO98005140 for ; Mon, 11 Aug 2003 14:30:24 -0400 Received: (from uucp@localhost) by mail-shield1.njit.edu (8.11.6/8.11.6) id h7BIUcM10439 for ; Mon, 11 Aug 2003 14:30:38 -0400 (EDT) Received: from nodnsquery(128.235.251.32) by mail-shield1.njit.edu via csmap (V4.1) id srcAAAxoayyu; Mon, 11 Aug 03 14:30:37 -0400 Received: from webmail.njit.edu (webmail.njit.edu [128.235.251.121]) by mail-gw4.njit.edu (8.12.9/8.12.4) with ESMTP id h7BIUan8006180 for ; Mon, 11 Aug 2003 14:30:36 -0400 (EDT) Received: (from apache@localhost) by webmail.njit.edu (8.11.7+Sun/8.11.7) id h7BILTX27428 for chemistry*at*ccl.net; Mon, 11 Aug 2003 14:21:29 -0400 (EDT) To: chemistry*at*ccl.net Subject: Random Search in SYBYL- Symmetry option Message-ID: <1060626089.3f37dea9494e4*at*webmail.njit.edu> Date: Mon, 11 Aug 2003 14:21:29 -0400 (EDT) From: dnp5*at*njit.edu References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.4 X-Originating-IP: 128.235.154.221 Hello: I would like to know the effect of symmetry option on and off on random search in Sybyl. > From Tripos bookshelf and the references mentioned it is clear to me how random search works and check chirality option functions but I do not understand how check symmetry option works. Thank you very much in advance. Sincerely, Deepangi Pandit From chemistry-request@ccl.net Mon Aug 11 13:06:16 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BH6E98001500 for ; Mon, 11 Aug 2003 13:06:15 -0400 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h7BH6Oej012733 for ; Mon, 11 Aug 2003 19:06:24 +0200 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h7BH6O0T012726 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 11 Aug 2003 19:06:24 +0200 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id h7BH6NSI006411 for ; Mon, 11 Aug 2003 19:06:23 +0200 Date: Mon, 11 Aug 2003 19:06:23 +0200 (CEST) From: Faza Olalla Nieto X-X-Sender: To: Subject: eigenvector following in MNDO97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Does anyone know how to make an optimization to a TS using the eigenvector following method with mndo97? When I try the combination of keywords jop=4 (in fact jop=anything) and ef=3 (I want to use the mode=3 afterwards) the program produces an error message that says that I have indicated too many options for the geometry optimization. I would really welcome any help on this subject. Regards Olalla Nieto Faza Dpto. Quimica Organica Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain) e-mail: faza*at*uvigo.es From chemistry-request@ccl.net Mon Aug 11 10:20:10 2003 Received: from mailhub1.shef.ac.uk (mailhub1.shef.ac.uk [143.167.1.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BEK998027583 for ; Mon, 11 Aug 2003 10:20:10 -0400 Received: from yateholme.shef.ac.uk ([143.167.248.9]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 19mDX5-00078x-00 for CHEMISTRY*at*ccl.net; Mon, 11 Aug 2003 15:20:23 +0100 Received: from YATEHOLME/SpoolDir by yateholme.shef.ac.uk (Mercury 1.48); 11 Aug 03 15:20:23 +0100 Received: from SpoolDir by YATEHOLME (Mercury 1.48); 11 Aug 03 15:20:15 +0100 Received: from NICKRHODESXP (143.167.102.126) by yateholme.shef.ac.uk (Mercury 1.48) with ESMTP; 11 Aug 03 15:20:09 +0100 From: "Nick Rhodes" Organization: CISRG, Information Studies To: CHEMISTRY*at*ccl.net Date: Mon, 11 Aug 2003 15:20:08 +0100 MIME-Version: 1.0 Subject: CCL: Conference announcement: Chemoinformatics Sheffield 2004 Message-ID: <3F37B428.19035.19D5C984@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.02a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body First announcement for The Third Joint Sheffield Conference on Chemoinformatics 21-23 April 2004 The conference will be held at the Octagon Centre and Tapton Hall of Residence, The University of Sheffield, UK. The meeting is sponsored by the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. The call for papers will be announced later in summer and further details will be placed on http://cisrg.shef.ac.uk/shef2004/ ***************************************************************** Nick Rhodes (Programme Development Officer, MSc Chemoinformatics), Computational Information Systems Research Group, Department of Information Studies, University of Sheffield, Regent Court, 211 Portobello Street, Sheffield, South Yorkshire, S1 4DP, United Kingdom. ------------- Hallam Grange Lawn Tennis Club http://www.hallamgrange.org.uk From chemistry-request@ccl.net Mon Aug 11 10:31:49 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7BEVm98028162 for ; Mon, 11 Aug 2003 10:31:49 -0400 Received: from psi.qmul.ac.uk ([138.37.7.6] helo=psi) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 19mDiM-0001zd-BH for chemistry-.at.-ccl.net; Mon, 11 Aug 2003 15:32:02 +0100 Received: from httpd by psi with local (Exim 3.31 #1) id 19mDiM-000666-00 for chemistry-.at.-ccl.net; Mon, 11 Aug 2003 15:32:02 +0100 Received: from 138.37.43.64 ( [138.37.43.64]) as user ezw079-.at.-imap.qmul.ac.uk by webapps.qmul.ac.uk with HTTP; Mon, 11 Aug 2003 15:32:02 +0100 Message-ID: <1060612322.3f37a8e20c3c8-.at.-webapps.qmul.ac.uk> Date: Mon, 11 Aug 2003 15:32:02 +0100 From: Ru-Zhen Li To: chemistry-.at.-ccl.net Subject: still question about BABEL MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 138.37.43.64 X-Sender-Host-Address: 138.37.7.6 X-QM-Scan-Accept: This message was accepted by ls_accept.so Dear all, Thank you for all the kind help. now, I have done it again from the very beginning, problem still exist 1)I downloaded babel106.zip from ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ 2)I unziped it, and copied the BABEL.EXE, ELEMENT.LIS, TYPE.LIS to C:\BABEL 3)I add SET BABEL_DIR=C:\BABEL to the AUTOEXEC.BAT which is in C:\Documents and Settings\ezw079.MATDOM\My Documents\My Received Files\winxpbootdisk\winxpbootdisk\HPWinXPbootdisk\WindowsXP&(&;+&\ 4)I copy the 1N5U.pdb in to C:\BABEL 5)I entered the C:\BABEL under dos typed babel -ip 1N5U.pdb -ocache output.csf nothing happened, no error, no waring, no output. and I tried Open BABEL, but seems it is under Unix not DOS or Win Thank you in advance for your help! regards, Ru-Zhen -- ========================= Ru-Zhen Li +44 020 7882 6327 Materials Department Queen Mary College University of London Mile End Road London E1 4NS