From chemistry-request@server.ccl.net Thu Sep 12 05:07:01 2002 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8C970326892 for ; Thu, 12 Sep 2002 05:07:01 -0400 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by dobit2.rug.ac.be (8.11.1/8.11.1) with ESMTP id g8C970Y16595 for ; Thu, 12 Sep 2002 11:07:00 +0200 (MEST) Received: from rug.ac.be (moldyn24.rug.ac.be [157.193.98.229]) by allserv.rug.ac.be (8.11.1/8.11.1) with ESMTP id g8C96uW28994 for ; Thu, 12 Sep 2002 11:06:56 +0200 (MEST) Message-ID: <3D8058C1.4080005@rug.ac.be> Date: Thu, 12 Sep 2002 11:05:05 +0200 From: Ewald Pauwels User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problem with Gaussian98 and duals Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, We have encountered some very weird problems with the Gaussian 98 software, and I would like to know if anybody else has had similar problems (and possible work-arounds). At our laboratory we run gaussian mainly on dual-processor linux computers (we do not perform parallel calculations with Linda, however). On several of our duals, we have noticed that G98 aborts simple geometry optimisation jobs after about 6 hours. It basically just stops in the SCF-procedure and does not report any error-messages. The weird part is that the same job runs perfectly on other duals, with exactly the same hardware and software configuration! We have solved this problem for some of our machines by replacing the motherboard, which is apparently causing these (seemingly random) aborts. However, we do not have a clue what the exact problem is with these motherboards (try explaining this to your vendor). On the other hand, ADF runs fine on these machines, so my guess is that it has something to do with Gaussian conflicting with some motherboard-problem. Many thanks for any help or comments on this matter. Sincerely, Ewald Pauwels Laboratory of Theoretical Physics Ghent University ewald.pauwels@rug.ac.be From chemistry-request@server.ccl.net Thu Sep 12 05:30:48 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8C9Ul327158 for ; Thu, 12 Sep 2002 05:30:48 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id LAA11688 for ; Thu, 12 Sep 2002 11:32:48 +0200 (MDT) Date: Thu, 12 Sep 2002 11:32:48 +0200 From: Per Tetzschner Olsen To: chemistry@ccl.net Subject: Reaction Distance Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Just one of those philosophical questions. I have heard plenty of rumors of different reaction distances, but have no references. Considering a molecule with an internal local reaction, what would the preferred reaction distance be for a nucleophilic reaction? - 2.5-3.0 Angstrom ? - about 3 Angstrom ? - 3.0-4.0 Angstrom ? - The distance between the active atoms in the transition structure + 1.0 Angstrom ? Statistical there is a better chance of reaction when the reaction distance is "short". Any reference or just comment is gladly accepted. Regards Per Dept. of Chemistry University of Southern Denmark DK-5230 Odense M From chemistry-request@server.ccl.net Thu Sep 12 09:33:52 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CDXq331321 for ; Thu, 12 Sep 2002 09:33:52 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g8CDXpq09965 for ; Thu, 12 Sep 2002 06:33:51 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 4687; Thu, 12 Sep 2002 06:34:19 -0700 (PDT) Received: from renoir.scripps.edu (renoir.scripps.edu [137.131.252.25]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g8CDXeO22470; Thu, 12 Sep 2002 06:33:40 -0700 (PDT) Received: from localhost (crowley@localhost) by renoir.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id GAA1205329; Thu, 12 Sep 2002 06:33:40 -0700 (PDT) Date: Thu, 12 Sep 2002 06:33:39 -0700 From: Michael Crowley To: Alice NgarKit Ko cc: chemistry@ccl.net Subject: Re: CCL:charmm size In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Alice, It may be that you are not recompiling from scratch. Once the pref.dat is made in the build// directory, it is not overwritten with another install.com command. If you want to be sure you are getting a new executable with new keywords (such as XLARGE) in the pref.dat, you should mv exec//charmm exec//charmm_large /bin/rm lib//* vi build//pref.dat *** fix LARGE to be what you want *** install.com xxlarge where whatever machine you specify in the install.com Or, make a new charmm tree and recompile there. If this is not the problem, please elaborate on what you did to try to get the xlarge. Sincerely, 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@scripps.edu Telephone: 858/784-9290 Fax: 858/784-8688 ----------------------------------------------------------------- On Wed, 11 Sep 2002, Alice NgarKit Ko wrote: > Hi, > > I tried to compile charmm with different sizes but it gives me the same > Maximum number of ATOMS: 25140, and RESidues: 14000. > > It doesn't matter whether I use xxlarge, large, medium or small. > > Anyone knows why? > > Thanks > > Alice > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Thu Sep 12 10:22:37 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CEMb332589 for ; Thu, 12 Sep 2002 10:22:37 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.6/8.12.6/Guy-23-01-2002) with ESMTP id g8CEMRrZ026007 for ; Thu, 12 Sep 2002 16:22:28 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id QAA15266 for ; Thu, 12 Sep 2002 16:21:37 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3D80A208.9FBD7F8E@lctn.uhp-nancy.fr> Date: Thu, 12 Sep 2002 16:17:44 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Lowdin atomic charges Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Dear CCLers, I am looking for the reference of the seminal paper concerning "Lowdin atomic charges". I even wonder if it was written by Lowdin himself. Many thanks. Yours. -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Sep 12 11:02:10 2002 Received: from rwcrmhc51.attbi.com ([204.127.198.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CF2A300864 for ; Thu, 12 Sep 2002 11:02:10 -0400 Received: from C1353359A ([12.228.112.246]) by rwcrmhc51.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020912150204.NEKS10266.rwcrmhc51.attbi.com@C1353359A> for ; Thu, 12 Sep 2002 15:02:04 +0000 Reply-To: From: "Mark Thompson" To: Subject: Autodock on Windows? Date: Thu, 12 Sep 2002 08:00:50 -0700 Message-ID: <001301c25a6d$2f049600$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Has anyone compiled/converted AutoDock 3.x to run on Windows? Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= From chemistry-request@server.ccl.net Thu Sep 12 12:07:21 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CG7L302504 for ; Thu, 12 Sep 2002 12:07:21 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17pWQu-0007SP-00; Thu, 12 Sep 2002 16:03:08 +0000 Date: Thu, 12 Sep 2002 16:03:07 +0000 (GMT) From: Szilveszter Juhos To: Mark Thompson cc: CHEMISTRY@ccl.net Subject: Re: CCL:Autodock on Windows? In-Reply-To: <001301c25a6d$2f049600$0300a8c0@attbi.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 12 Sep 2002, Mark Thompson wrote: > Has anyone compiled/converted AutoDock 3.x to run on Windows? Though I am not using windows for ages, try CygWin http://www.cygwin.com/ , one of my friends successfully compiled a lot of UNIX stuff with it (and it is free :). Cheers Szilva From chemistry-request@server.ccl.net Thu Sep 12 14:03:59 2002 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CI3x305577 for ; Thu, 12 Sep 2002 14:03:59 -0400 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g8CI3mQn001817 for ; Thu, 12 Sep 2002 11:03:48 -0700 Received: FROM dante40.u.washington.edu BY mailscan-out2.cac.washington.edu ; Thu Sep 12 11:03:47 2002 -0700 Received: from localhost (jzheng73@localhost) by dante40.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.08) with ESMTP id g8CI3lMl111578 for ; Thu, 12 Sep 2002 11:03:47 -0700 Date: Thu, 12 Sep 2002 11:03:47 -0700 (PDT) From: "J. Zheng" cc: CCL Subject: TIP3P model in charmm In-Reply-To: <3D80A208.9FBD7F8E@lctn.uhp-nancy.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers: The TIP3P water model in the charmm is differnt from the standard TIP3P model. the hydrogen of water in the charmm has the well depth and radius, which both are set to 0.0 in the standard TIP3P model. Now, I am wondering that in the charmm, for water-protein interactions, it uses this modified TIP3P model. but for water-water interactions, it uses standard TIP3P model, that is, there is no interaction between O and H for different water molecules. OR, it uses this modified TIP3P model to calculate water-protein and water-water interactions. which way charmm go? I will apreciate anyone to clarify this puzzle. jie ----------------------------------------------- | JIE ZHENG | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 616-6510 (o) | | Email: jzheng73@u.washington.edu | | Webpg: students.washington.edu/jzheng73 | ----------------------------------------------- From chemistry-request@server.ccl.net Thu Sep 12 17:41:41 2002 Received: from hydrant.ruf.rice.edu ([128.42.31.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CLff309469 for ; Thu, 12 Sep 2002 17:41:41 -0400 Received: from spca.ruf.rice.edu (spca.ruf.rice.edu [128.42.31.11]) by hydrant.ruf.rice.edu (Postfix) with ESMTP id C9EDF33422 for ; Thu, 12 Sep 2002 16:41:40 -0500 (CDT) Received: from localhost (kostya@localhost) by spca.ruf.rice.edu (8.9.0/8.9.0) with ESMTP id QAA18542 for ; Thu, 12 Sep 2002 16:41:40 -0500 (CDT) Date: Thu, 12 Sep 2002 16:41:35 -0500 (CDT) From: "Konstantin N. Kudin" X-X-Sender: To: Subject: Visualization of arbitrary numbers on each atom Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues Is there any visualization packages out there that could display some numbers assigned to atoms in a structure? For example, I would like to vizualize Mulliken charges assigned to each atom with the amount of charge being indicated by color or by something else. Thanks! Regards, Konstantin Kudin P.S. If there is sufficient interest, I will summarize. From chemistry-request@server.ccl.net Thu Sep 12 19:34:53 2002 Received: from theopzs.chem.elte.hu ([157.181.193.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8CNYr316530 for ; Thu, 12 Sep 2002 19:34:53 -0400 Received: by theopzs.chem.elte.hu (Postfix, from userid 1321) id 94E917C1E; Fri, 13 Sep 2002 01:30:39 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by theopzs.chem.elte.hu (Postfix) with ESMTP id 796A17C02 for ; Fri, 13 Sep 2002 01:30:39 +0200 (CEST) Date: Fri, 13 Sep 2002 01:30:39 +0200 (CEST) From: Zsolt Szekeres To: chemistry@ccl.net Subject: Re: CCL:Visualization of arbitrary numbers on each atom In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Is there any visualization packages out there that could display > some numbers assigned to atoms in a structure? > OpenDX is a general purpose scientific visualization tool. Have a look at www.opendx.org! Zsolt Szekeres