From chemistry-request@server.ccl.net Tue Sep 17 04:52:31 2002 Received: from mistral.genodyssee.com ([213.56.212.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8H8qUw08303 for ; Tue, 17 Sep 2002 04:52:31 -0400 Received: from aquilon.genodyssee.com (aquilon.genodyssee.com [213.56.212.34]) by mistral.genodyssee.com (8.12.3/8.12.3) with ESMTP id g8H8qPNA006644 for ; Tue, 17 Sep 2002 10:52:30 +0200 (MEST) Content-Type: text/plain; charset="us-ascii" From: Xavier Gallet To: chemistry@ccl.net Subject: protein side-chains Date: Tue, 17 Sep 2002 10:52:25 +0200 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200209171052.25581.gallet@genodyssee.com> Dear CCLers, Does anyone known some reference articles or databases available on the web concerning statistics about protein side-chains interactions (frequency, distance, orientations, ...). I already know the relevant 'Atlas of Protein side-chains interaction" (http://www.biochem.ucl.ac.uk/bsm/sidechains/) of J.Thornton, but I would be curious to known whether other similar websites exist. Regards, Xavier Gallet From chemistry-request@server.ccl.net Tue Sep 17 05:58:29 2002 Received: from mail-f.bcc.ac.uk ([128.40.23.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8H9wTw09243 for ; Tue, 17 Sep 2002 05:58:29 -0400 Received: from dale.ri.ac.uk by mail-f.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 17 Sep 2002 10:58:28 +0100 Received: from ri.ac.uk (davy.ri.ac.uk) by dale.ri.ac.uk (Content Technologies SMTPRS 4.1.5) with SMTP id for ; Tue, 17 Sep 2002 10:50:44 +0100 Received: from tyndall.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA27446; Tue, 17 Sep 2002 10:58:26 +0100 Received: from localhost by tyndall.ri.ac.uk (980427.SGI.8.8.8) id KAA27953; Tue, 17 Sep 2002 10:58:18 +0100 (BST) Date: Tue, 17 Sep 2002 10:58:18 +0100 From: Naseem Ramsahye To: chemistry@ccl.net Subject: Restarting Gaussian jobs Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am having a bit of trouble restarting a Guassian job. I have all the files (rwf, chk etc), but the calculation (single point) did not finish, and I cannot seem to restart the SCF. It seems not to be able to read the checkpoint file. Just to check, is it possible to restart such a calc in Gaussian? ie one where the first set of SCF cycles have not yet converged? Many thanks in advance for any and all help/advice offered. Regards Naseem ------------------------------------------------------------------------ Naseem A. Ramsahye Research Student, DFRL Royal Institution of Great Britain, 21 Albemarle Street, LONDON W1S 4BS Tel: 020 7409 2992 Email: naseem@ri.ac.uk Website: http://www.ri.ac.uk/DFRL *** The RI is a Registered Charity (Number 227938) *** ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Sep 17 07:15:23 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 g8HBFNw10346 for ; Tue, 17 Sep 2002 07:15:23 -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 g8HBFMGP028404 for ; Tue, 17 Sep 2002 08:15:22 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Tue Sep 17 08:15:22 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 IAA21830; Tue, 17 Sep 2002 08:15:21 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Tue, 17 Sep 2002 08:15:21 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List , Venkataraman Kabaleeswaran X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:autodock Message-ID: <3D887F58@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hi Venkataraman, The Autodock group has developed a set of tools called AutodockTools (ADT) which provides a graphical interface and makes setting up the Autodock files and docking jobs fairly straightforward and simple. There is a link to the ADT download site from the main Autodock page. ADT will run in Unix, Linux, and Windows. ADT also provides simple charge calculations for the receptor, and the ability to view the output of the docking run. If you have any problems getting ADT to run, do not hesitate to send me an e-mail. cheers, Robert >===== Original Message From Venkataraman Kabaleeswaran ===== >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 ******************************** 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 Tue Sep 17 08:47:16 2002 Received: from titanium.mater.unimib.it (root@[149.132.101.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HClFw12436 for ; Tue, 17 Sep 2002 08:47:15 -0400 Received: from rutenio.mater.unimib.it (rutenio.mater.unimib.it [149.132.99.56]) by titanium.mater.unimib.it (8.9.3 (PHNE_22672)/8.9.3) with ESMTP id OAA08569; Tue, 17 Sep 2002 14:47:48 +0200 (METDST) Message-Id: <5.1.0.14.0.20020917143614.02483730@titanium.mater.unimib.it> X-Sender: narducci@titanium.mater.unimib.it X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 17 Sep 2002 14:47:07 +0200 To: chemistry@ccl.net From: Dario Narducci Subject: frequency calculations using MP2 in Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 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 ============================== From chemistry-request@server.ccl.net Tue Sep 17 09:58:33 2002 Received: from rockridge.uits.indiana.edu ([129.79.1.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8HDwXw14128 for ; Tue, 17 Sep 2002 09:58:33 -0400 Received: from jade.iupui.edu (jade.iupui.edu [134.68.220.114]) by rockridge.uits.indiana.edu (8.12.1/8.12.1/IUPO) with ESMTP id g8HDwVn1022076 for ; Tue, 17 Sep 2002 08:58:31 -0500 (EST) Received: from localhost (qzou@localhost) by jade.iupui.edu (8.10.1/8.10.1/jade.20020708) with SMTP id g8HDwWJ17624 for ; Tue, 17 Sep 2002 08:58:32 -0500 (EST) X-Authentication-Warning: jade.iupui.edu: qzou owned process doing -bs Date: Tue, 17 Sep 2002 08:58:32 -0500 (EST) From: Qin Zou To: chemistry@ccl.net Subject: clear my previous question on ADT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry I did not make it clear that I was trying to increase the maximum number of GA runs. Hope anyone out there has a clue. Thanks. Q.