From chemistry-request@ccl.net Tue Nov 4 02:00:58 2003 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA470RhP028439 for ; Tue, 4 Nov 2003 02:00:27 -0500 Received: from 192.168.0.101 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id hA470QJI019274 for ; Mon, 3 Nov 2003 23:00:26 -0800 Date: Mon, 3 Nov 2003 23:59:54 -0800 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1826833770.20031103235954)at(joyie.com> To: chemistry)at(ccl.net Subject: disk space error MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCIrvine-MailScanner: No viruses found X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers After a g03 simulation, I got the following error message: **** Warning!!: The largest alpha MO coefficient is 0.13620479D+02 Disk-based method using ON**2 memory for 16 occupieds at a time. Permanent disk used for amplitudes= 59913420 words. Estimated scratch disk usage= 1039185760 words. Actual scratch disk usage= 1031867744 words. Erroneous write during file extend. write 221183 instead of 4096 Probably out of disk space. Erroneous write during file extend. write 221183 instead of 4096 Probably out of disk space. Write error in NtrExt1 Write error in NtrExt1: Success The disk still has enough space (50G, 46G available). What caused this problem? -- Best regards, John Lee From chemistry-request@ccl.net Tue Nov 4 02:00:33 2003 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4700hP028422 for ; Tue, 4 Nov 2003 02:00:01 -0500 Received: from 192.168.0.101 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id hA46xpJI019055 for ; Mon, 3 Nov 2003 22:59:54 -0800 Date: Mon, 3 Nov 2003 23:50:51 -0800 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1614539587.20031103235051)at(joyie.com> To: chemistry)at(ccl.net Subject: questions about optimization with gaussian MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCIrvine-MailScanner: No viruses found X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, I have two questions about optimization. 1, For partial optimization, there could be only stationary point? 2, The optimization we used the most and the default one in gaussian is based on harmonic model or not? -- Best regards, John Lee From chemistry-request@ccl.net Mon Nov 3 22:43:32 2003 Received: from einstein.physics.drexel.edu (einstein.physics.drexel.edu [129.25.7.60]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA43h0hP023578 for ; Mon, 3 Nov 2003 22:43:00 -0500 Received: from si (silicon.physics.drexel.edu [129.25.8.33]) by einstein.physics.drexel.edu (8.11.6/8.11.6) with ESMTP id hA43aeK05693 for ; Mon, 3 Nov 2003 22:36:40 -0500 Date: Mon, 3 Nov 2003 22:42:58 -0500 (EST) From: Avijit Ghosh To: chemistry)at(ccl.net Subject: Re: CCL:Linux Cluster In-Reply-To: <3FA6047B.4070200)at(chem.vu.nl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) We just bought our cluster from a vendor (Western Scientific). I would recommend going to a vendor if you can afford it, mostly to guarantee there won't be any hardware incompatibilities that are sometimes hard to work out until you start setting everything up. Hardware Linux vendors will also quite possibly be more up to date on what the best configurations/tools might be. Price it out and take a look at the relative costs of going the "do it yourself" route and from a vendor. (In our case, our prices were pretty competitive w/ buying cheap 1U dual xeon blades from bulk hardware companies like www.mwave.com and the support is absolutely brilliant). If it looks like it is much cheaper going the do it yourself route, take a look at the following: http://oscar.openclustergroup.org/tiki-index.php Oscar will automate installation over a network and make it reasonably straightforward to install over an arbitrary number of nodes, setup a reasonable queueing system, install mpi(ch), take care of user accounts and maintain patches/updates. The documentation provides some good advice on "reasonable" configurations as well. Read over the "quick install" to get a sense of the work involved for setting up a cluster on your own. Its quite impressive how straightforward this stuff has become. There is no 6 node limit :) best regards, -avi Asst. Prof. Avijit Ghosh, Ph.D. Dept of Physics Drexel University Philadelphia, PA 19104 From chemistry-request@ccl.net Tue Nov 4 03:16:07 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA48FahP031525 for ; Tue, 4 Nov 2003 03:15:36 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AGwLf-000NIDC; Tue, 4 Nov 2003 09:15 +0100 Message-ID: <3FA760E7.6090001.-at-.chem.vu.nl> Date: Tue, 04 Nov 2003 09:18:47 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 CC: chemistry.-at-.ccl.net Subject: Re: CCL:disk space error References: <1826833770.20031103235954.-at-.joyie.com> In-Reply-To: <1826833770.20031103235954.-at-.joyie.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.6 required=7.0 tests=IN_REP_TO,MISSING_HEADERS,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) John Lee wrote: [...] > Estimated scratch disk usage= 1039185760 words. > Actual scratch disk usage= 1031867744 words. [...] > The disk still has enough space (50G, 46G available). What caused this > problem? It seems like you're writing 1G words, which would be 2G bytes. Perhaps your filesystem (or other OS components) doesn't support files >2Gb? -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Tue Nov 4 03:30:08 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA48TbhP032157 for ; Tue, 4 Nov 2003 03:29:37 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AGwZE-000NIDC; Tue, 4 Nov 2003 09:29 +0100 Message-ID: <3FA76430.1060007.-at-.chem.vu.nl> Date: Tue, 04 Nov 2003 09:32:48 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: Re: CCL:Linux Cluster References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Avijit Ghosh wrote: > We just bought our cluster from a vendor (Western Scientific). > I would recommend going to a vendor if you can afford it, mostly > to guarantee there won't be any hardware incompatibilities that > are sometimes hard to work out until you start setting everything up. > > Hardware Linux vendors will also quite possibly be more up to date > on what the best configurations/tools might be. If I may add some (hard-learned) notes about do's and dont's in hardware: - check linux support for your networkcard - check for available options in the bootrom of your networkcard (if you're going to use that, you probably would want to) - get a reliable motherboard (don't go for the cheapest) - oreder the boxes pre-installed with your flavor of linux, that eliminates a number of possible (trivial, but annoying and time-consuming) harware problems (like loose cable connectors, or memory banks...) Run a memory test and cpu-burn when you get the machines. (I've spent months configuring and re-configuring my first two nodes, which turned out to be faulty...) - get boxes with lots of holes and put fans in all of the holes (get the expensive ball bearing ones, too, others fail too soon). See to it that cables don't obstruct airflow in the box. - do install a graphics card - wonderful if you need to find strange errors. - don't get an (expensive) keyboard/graphics switch. Plugging cables also works. - using dual CPU machines saves you in operating cost - less hardware to maintain. - if floorspace is not an issue, boxes on shelves do just as well as 19" rackmounted stuff. Well, maybe this is all too obvious to most of you, but I've seen people making, well let's call it 'less well-informed decisions' about buying cluster hardware, so I thought I'd just add my two-cents... -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Tue Nov 4 03:51:42 2003 Received: from sungod.ccs.yorku.ca (mailrelay.yorku.ca [130.63.236.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA48pAhP001202 for >ccl.net>; Tue, 4 Nov 2003 03:51:10 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.12.10/8.12.8) with ESMTP id hA48p9YU017317 for >ccl.net>; Tue, 4 Nov 2003 03:51:09 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id hA48kmv22499 for chemistry<>ccl.net; Tue, 4 Nov 2003 03:46:48 -0500 (EST) From: Wai-To Chan >curl.gkcl.yorku.ca> Message-Id: <200311040846.hA48kmv22499<>curl.gkcl.yorku.ca> Subject: Tips on how to locate TS structures To: chemistry<>ccl.net Date: Tue, 4 Nov 2003 03:46:48 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Assuming you have a reaction similar to the ring-opening of the simplest epoxide the oxirane, cyc-CH2OCH2 ---> H2CCH2O, here are the possible difficulties you have to consider. The ring-opening reaction is the decomposition of a closed-shell molecule into a singlet diradical. The TS structure could be a partial diradical. Depending on the type of method you are using the TS has to be located using either an unrestricted or restricted method. If you are using an unrestricted method searching for a partial diradical in the vicinity of a closed-shell structure chance is that the unrestricted solution could collapse to the closed-shell restricted solution during the course of geometry(TS) optimization. The reaction is in some way similar to a bond fission reaction. Just picture the coupling of the two odd electrons in the ring-closure reaction. One can imagine that the energy would fall off rapidly as the diradical transforms into a closed-shell structure. It is possible that there is no well-defined TS structure for your reaction. If you think the above deduction applies to your situation it is better to check out first studies of similar system > from recent literature before you proceed with your calculations. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<<<<, hi, CCL users: I am now trying to locate a TS struture of an epoxide ring open reaction. But I failed many times using QST2 and QST3 method to locate it. I even failed to optimize a "guess" structure which is supposed to be a saddle point on potential energy surface to TS structure. Could anyone give me some tips on how to locate a TS structure effectively? Is there any general procedure to do that? (e.g. do I need a PES scan ? ) Any suggestions would be highly appreciated! Have a good day. Cheers Yong L. Y. >>>>>>>>>>>>>>>>>>>>>>>>>>>> From chemistry-request@ccl.net Tue Nov 4 06:39:52 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4BdLhP008417 for ; Tue, 4 Nov 2003 06:39:21 -0500 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Tue, 4 Nov 2003 11:39:09 +0000 Date: Tue, 4 Nov 2003 11:39:09 +0000 Message-ID: <3F6B7AEB0003CDEC..at..hawk.dcu.ie> In-Reply-To: <1826833770.20031103235954..at..joyie.com> From: "Noel O'Boyle" Subject: RE: CCL:disk space error To: "John Lee" Cc: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hA4BdqhP008450 Hello John, Gaussian seems to impose a limit of 2GB on the size of read-write files. To get around this you need to specify a number of read-write files as Link 0 commands, i.e. %rwf=gxx1.rwf,2000MB,gxx2.rwf,2000MB,gxx3.rwf,2000MB I think there is also a limit on the number of read-write files you can create. Noel O'Boyle From chemistry-request@ccl.net Tue Nov 4 08:47:52 2003 Received: from mtiwmhc11.worldnet.att.net (mtiwmhc11.worldnet.att.net [204.127.131.115]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4DlJhP012744 for ; Tue, 4 Nov 2003 08:47:20 -0500 Received: from daveg-lifebook.cachesoftware.com (81.mercerville-31-32rs.nj.dial-access.att.net[12.94.172.81]) by worldnet.att.net (mtiwmhc11) with SMTP id <2003110413471711100rmde6e>; Tue, 4 Nov 2003 13:47:18 +0000 Message-Id: <5.2.1.1.0.20031104051716.0265a490-.at.-wheresmymailserver.com> X-Sender: X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Tue, 04 Nov 2003 05:31:42 -0800 To: "CCL" From: David Gallagher Subject: CCL:Tips on how to locate TS structures Cc: "yonyang" Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.4 required=7.0 tests=QUOTED_EMAIL_TEXT,RCVD_IN_NJABL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Yong, I have been able generate transition states and complete reaction paths for the first two probable steps for acid catalyzed epoxide ring opening (protonation by the methylammonium+ ion, followed by epoxide ring opening) > from the files you sent me. I shall attach the two transition state structures to you in a separate email. All calculations were done with PM3 gas phase (for speed), using CAChe MOPAC 2002. However, a COSMO solvent calculation would probably be more realistic if you are trying to simulate the reaction in solution. The transition states were confirmed by a single negative vibration (FORCE calculation), followed by intrinsic reaction coordinates (IRCs) to confirm no other intermediates. We have a complete tutorial for reaction modelling with CAChe available, let me know if you need a copy. The next step would be to explore the subsequent reaction steps in a simplified form and, finally, combine them all into one system. At that point you could test if the reaction is concerted or stepwise, by running IRCs from the transition states. These kinds of calculations are very easy to do from CAChe's graphical interface (about 1 hour to sketch and calculate all the reactants, products, transition states, and reaction paths for these two steps on a Windows laptop PC), but usually more difficult to do with a stand-alone quantum chemistry package. I hope this helps. Let me know if you need any further information. Regards, David Gallagher CAChe Group, Fujitsu >----- Original Message Follows ----- > > Hi Yong, > > > > When protonated, some epoxides can ring open with very little > > activation energy. However, the automated tools in CAChe MOPAC 2002 > > are usually quite good at finding transition states. If you send me > > the complete reactant and product structures (sketch or 3D files) > > we'll try and locate the TS geometry for you. Is it in gas phase or a > > solvent? Then, if you wish, you could use it as a starting structure > > for refinement with an alternative method. There is a brief guide to > > locating TS structures with CAChe MOPAC at > > http://www.cachesoftware.com/pdfs/CACheGuideTransitionStateModel.pdf > > > > Regards, > > David Gallagher > > CAChe Group, Fujitsu > > > > > > At 09:50 AM 10/31/2003 -0500, Yong Liang Yang wrote: > > > > >hi, CCL users: > > > > > >I am now trying to locate a TS struture of an epoxide > > >ring open reaction. But I failed many times using > > >QST2 and QST3 method to locate it. I even failed to > > >optimize a "guess" structure which is supposed to be > > >a saddle point on potential energy surface to TS structure. > > >Could anyone give me some tips on how to locate a TS structure > > >effectively? Is there any general procedure to do that? > > >(e.g. do I need a PES scan ? ) Any suggestions would be > > >highly appreciated! Have a good day. > > > > > > > > >Cheers > > > > > >Yong L. Y. > > > > > > > > > > > > > > >-= This is automatically added to each message by the mailing script > > =- >To send e-mail to subscribers of CCL put the string CCL: on your > > Subject: line >and send your message to: CHEMISTRY-.at.-ccl.net > > > > > >Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST-.at.-ccl.net >HOME Page: http://www.ccl.net | Jobs > > Page: http://www.ccl.net/jobs > > > >If your mail is bouncing from CCL.NET domain send it to the > > maintainer: >Jan Labanowski, jkl-.at.-ccl.net (read about it on CCL Home > > Page) > > >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+ > > > From chemistry-request@ccl.net Tue Nov 4 12:05:26 2003 Received: from uis-gumail-2.georgetown.edu (postoffice-2.georgetown.edu [141.161.1.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4H4shP021985 for ; Tue, 4 Nov 2003 12:04:54 -0500 Received: from georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by uis-gumail-2.georgetown.edu (8.12.10/8.12.10) with ESMTP id hA4H4ZqX010676; Tue, 4 Nov 2003 12:04:35 -0500 (EST) From: To: Cc: chemistry/at/ccl.net Message-ID: <3ef173bda2.3bda23ef17/at/georgetown.edu> Date: Tue, 04 Nov 2003 09:04:35 -0800 X-Mailer: Netscape Webmail MIME-Version: 1.0 Content-Language: en Subject: Re: CCL:Virtual screening X-Accept-Language: en Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-GU-FilterVersion: 1.22 X-Scanned-By: MIMEDefang 2.36 X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS,NO_REAL_NAME,QUOTED_EMAIL_TEXT, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Anil: Please refer the following web site: http://www.chem.ox.ac.uk/ hope you will get some input for your question. Siva D.Sivanesan, Ph.D. Dept. of Oncology, Lombardi Cancer Center (NCI Comprehensive Cancer Center), Georgetown University, DC 20057 Phone: 202-687-6338 ----- Original Message ----- From: Date: Thursday, October 30, 2003 7:47 am Subject: CCL:Virtual screening > Dear All, > > I was wondering whether there is any studies/statistics regarding > the success > of virtual screening (including docking and pharmacophore based > search)across different targets and/or target families. I have seen > severalpublications that compare different docking > softwares/scoring functions but I > am not aware of any discussion regarding the success rate using > pharmacophoresearch or docking approaches across various > targets/target families. I really > appreciate if someone could share their experiences or point me to the > references. > > I will summarize the answers if there is interest for it. > > Thanks a lot. > > -Anil. > > anil.nair/at/aventis.com > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY/at/ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer:Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home > Page)-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Nov 4 13:53:21 2003 Received: from smtp7.Stanford.EDU (smtp7.Stanford.EDU [171.67.16.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4IqT7P001873 for ; Tue, 4 Nov 2003 13:52:49 -0500 Received: from elaine28.Stanford.EDU (elaine28.Stanford.EDU [171.64.15.103]) by smtp7.Stanford.EDU (8.12.10/8.12.10) with ESMTP id hA4IpnVR005875 for ; Tue, 4 Nov 2003 10:51:51 -0800 (PST) Received: (from liviu@localhost) by elaine28.Stanford.EDU (8.12.10/8.12.9) id hA4IpjV8020928; Tue, 4 Nov 2003 10:51:45 -0800 (PST) Date: Tue, 4 Nov 2003 10:51:45 -0800 (PST) From: Liviu Mihail Mirica To: chemistry/at/ccl.net Subject: Error in freq job Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I have a problem completing a gaussian98 frequency job. I have a system with ~600 basis functions and the freq job quits with the following message: "Compute integral second derivatives. ... and contract with generalized density number 0. FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)= -690 Len= 1 IPos= 1 Q= 1089289192 dumping /fiocom/, unit = 1 NFiles = 78 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 667585536 FType=2 FMxFil=10000 .... (similar lists as below)... Number 989 993 997 998 Base 788700 791200 791300 23677 End 791200 791300 911304 23727 End1 791200 791300 911304 23727 Wr Pntr 788700 791200 791300 23677 Rd Pntr 788700 791200 791300 23677 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO." I have split the .rwf files to comply with the 2GB size limit, but it still quits before computing the integral second derivatives. Anyone has any idea about this? Any help will be appreciated. Thank you, Liviu Mirica ************************** Liviu Mihail Mirica tel: 650-497-3188 Escondido Village, 35 B email: liviu/at/leland.stanford.edu Stanford, CA 94305, USA From chemistry-request@ccl.net Tue Nov 4 09:56:49 2003 Received: from dalton.quimica.unlp.edu.ar (dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4EuAhP016825 for ; Tue, 4 Nov 2003 09:56:16 -0500 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.12.9/8.12.5) with ESMTP id hA4Eu4WC001498 for ; Tue, 4 Nov 2003 11:56:04 -0300 Message-Id: <5.1.0.14.2.20031104114319.009fd2f0/at/dalton.quimica.unlp.edu.ar> X-Sender: pis_diez/at/dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 04 Nov 2003 11:57:57 -0300 To: chemistry/at/ccl.net From: Reinaldo Pis Diez Subject: G98 and the 2 GB limit in Linux Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-AntiVirus: checked by AntiVir Milter 1.0.1; AVE 6.22.0.1; VDF 6.22.0.27 Dear folks, I've just (re)installed the RedHat 9 Linux distribution in our modest cluster using the SGI XFS installer cd to have the filesystems supporting files larger than the well-known 2 GB limit. A small test program (it writes the elements of a huge vector to a disk file) generates a ca. 2.7 GB file without crashing. I compiled the program with the 3.2.2 version of gcc. Unfortunately, when I tried a Gaussian98 job (a ccsd(t) geometry optimization on water using a cc-pvqz basis) to further test our XFS filesystem, it crashed when the rwf scratch file achieves a size of 2 GB. I must say that we only have the binaries of G98, Rev A.9, not compiled by us. Now the question: Is there any intrinsic limitation to 2 GB files in Gaussian98 running under Linux? Why a simple test program runs well but G98 fails against SGI XFS Linux? Thanks in advance. Regards, Reinaldo From chemistry-request@ccl.net Tue Nov 4 08:58:04 2003 Received: from smtp02.syd.iprimus.net.au (smtp02.syd.iprimus.net.au [210.50.76.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4DvVhP013643 for ; Tue, 4 Nov 2003 08:57:32 -0500 Received: from alex.roach (210.50.176.121) by smtp02.syd.iprimus.net.au (7.0.020) id 3F8F522A005DB58F for chemistry$at$ccl.net; Wed, 5 Nov 2003 00:57:30 +1100 Received: from alex by alex.roach with local (Exim 3.35 #1 (Debian)) id 1AH1oD-0007GO-00 for ; Wed, 05 Nov 2003 01:05:25 +1100 Date: Wed, 5 Nov 2003 01:05:24 +1100 To: chemistry$at$ccl.net Subject: blind docking of large protein molecules Message-ID: <20031104140524.GA27892@alex> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i From: Alex Sutcliffe X-Spam-Status: No, hits=-2.5 required=7.0 tests=USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I am interested in investigating potential dockings between protein molecules and only have pretty limited ideas about potential binding sites. I have toyed with autodock, zdock and hex with mixed results and am finding it a bit intensive resources wise. What packages or combinations there of do people recommend for this sort of thing? Since it does not seem feasible attempt to use both molecules in their entirety, I was thinking about splitting one into smaller chunks, ie grabbing chunks that are close to the surface and attempting to dock them in turn. Does anyone have any experience or tips from similar efforts or know of any papers etc detailing any efforts or methodologies that I might find useful? Thanks in advance! Alex Sutcliffe From chemistry-request@ccl.net Tue Nov 4 17:26:16 2003 Received: from sims.csuohio.edu (csu-mail0.csuohio.edu [137.148.5.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4MPYVc001207 for ; Tue, 4 Nov 2003 17:25:44 -0500 Received: from csuohio.edu (niobium.si-02-01.csuohio.edu [137.148.162.17]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0HNU0032DMAJSI_at_sims.csuohio.edu> for chemistry_at_ccl.net; Tue, 4 Nov 2003 17:25:31 -0500 (EST) Date: Tue, 04 Nov 2003 17:25:31 -0500 From: Daniela Dogaru Subject: CCL:ESP charges To: chemistry_at_ccl.net Message-id: MIME-version: 1.0 X-Mailer: Apple Mail (2.552) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I have a question regarding the ESP charges which are used in OPLS parameters from MD programs like Gromacs . I got some discrepancies between the OPLS charges I calculated with Gaussian and the ones that are implemented in Gromacs force field , for Tyrosine residue. What do you think will be the problem? My best wishes! Daniela From chemistry-request@ccl.net Tue Nov 4 16:30:22 2003 Received: from sims.csuohio.edu (csu-mail0.csuohio.edu [137.148.5.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4LTG7P006008 for ; Tue, 4 Nov 2003 16:29:51 -0500 Received: from csuohio.edu (niobium.si-02-01.csuohio.edu [137.148.162.17]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0HNU00NLF8W90Z~at~sims.csuohio.edu> for chemistry~at~ccl.net; Tue, 4 Nov 2003 12:36:11 -0500 (EST) Date: Tue, 04 Nov 2003 12:36:09 -0500 From: Daniela Dogaru Subject: ESP charges To: chemistry~at~ccl.net Message-id: <608AF095-0EED-11D8-8DC2-000393C8EB28~at~csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.552) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I have a question regarding the ESP charges which are used in OPLS parameters from MD programs like Gromacs . I got some discrepancies between the OPLS charges I calculate with Gaussian and the ones that are implemented in Gromacs force field , for Tyrosine residue. What do you think will be the problem? My best wishes! Daniela From chemistry-request@ccl.net Tue Nov 4 19:54:16 2003 Received: from etsuex1.etsu.edu (etsuex1.etsu.edu [151.141.8.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA50rhVc004626 for ; Tue, 4 Nov 2003 19:53:44 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3A337.433C4F10" Subject: Dual Xeon & G98 Date: Tue, 4 Nov 2003 19:53:44 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Dual Xeon & G98 Thread-Index: AcOjN0Nri5R34g5pEdiPpgBAlXb8og== From: "Close, David M." To: X-Spam-Status: No, hits=0.7 required=7.0 tests=HTML_70_80,HTML_FONT_COLOR_BLUE,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------_=_NextPart_001_01C3A337.433C4F10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL'ers: Someone told me I can run G98 jobs faster on my Dell 530 Workstation = if I use %Nproc=3D2 and make the following changes to the LINUX kernel = for sharing memory.=20 =20 echo "67108864" >/proc/sys/kernel/shmmax echo "67108864" >/proc/sys/kernel/shmall=20 =20 only replace 67108864 with the amount of memory in your machine (in = bytes) =20 Also, I know that the %Mem=3D should be per processor. Therefore, since = I have 512Mb total memory and 2 processors, I should use something like = %Mem=3D230Mb =20 Having done all this and also checking that the SMP kernel was running, = I cannot get this to work. After only a second the program quits where the list of links to be used = is printed. The program ends with an "shmget failed" statement. I = presume this has something to do with shared memory, but I am not sure = what to try next. Perhaps someone knows what to try next, or perhaps = what diagnostics to use to make sure the system has been configured properly. Regards, Dave Close. =20 =20 =20 ------_=_NextPart_001_01C3A337.433C4F10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

CCL’ers<= /span>:

=A0 Someone = told me I can run G98 jobs faster on my Dell 530 Workstation if I use %Nproc=3D2 and make the following changes to the = LINUX kernel for sharing memory.

 

echo "67108864" >/proc/sys/kernel/shmmax

echo "67108864" >/proc/sys/kernel/shmall

 

only replace 67108864 with the amount of memory in your machine (in = bytes)

 

Also, I know that the %Mem=3D should be per processor. Therefore, since I have 512Mb total memory and 2 = processors, =A0I = should use something like %Mem=3D230Mb

 

Having done all this and also checking that the SMP = kernel was running, I cannot get this to = work.

After only a second the program quits where the list = of links to be used is printed.=A0 = The program ends with an “shmget failed” statement.=A0 I presume this has something to do = with shared memory, but I am not sure what to try next.=A0 Perhaps someone knows what to try = next, or perhaps what diagnostics to use to make = sure

the system has been configured = properly.

=A0 Regards, Dave Close.=A0

 

 

=00 ------_=_NextPart_001_01C3A337.433C4F10-- From chemistry-request@ccl.net Tue Nov 4 16:27:19 2003 Received: from be-research.ucsd.edu (be-research.ucsd.edu [132.239.236.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4LQQ7P005865 for ; Tue, 4 Nov 2003 16:26:47 -0500 Received: from localhost (dsteiger@localhost) by be-research.ucsd.edu (8.11.1/8.11.1) with ESMTP id hA4LQFR11708546 for ; Tue, 4 Nov 2003 13:26:15 -0800 (PST) Date: Tue, 4 Nov 2003 13:26:15 -0800 From: Don Steiger To: chemistry~at~ccl.net Subject: Lennard Jones truncation error? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Does anybody know of any studies that look at the error in using a finite Lennard Jones cutoff radius? Thanks, Don dsteiger~at~bioeng.ucsd.edu From jkl@ccl.net Tue Nov 4 21:33:51 2003 -0500 Return-Path: Message-Id: <200311050220.KAA14732*at*mx1.ustc.edu.cn> Date: Wed, 5 Nov 2003 10:21:43 +0800 From: dxl*at*mail.ustc.edu.cn Reply-To: dxl*at*mail.ustc.edu.cn To: chemistry*at*ccl.net Subject: Bond order in gaussian Dear All I am try to do a bond order analysis with G98. Here is my test with O2 molecule. #B3LYP/6-31G opt pop=(NBO,Bonding) HF 0 3 O 0.00 0.00 0.000000 O 0.00 0.00 1.200000 The last lines of the output file is below, and I don't think it is right. How can I read the table correctly? And what the LP,RY* stand for? Thank you very much for your help!!!!!!!!!!!!!!!!! Natural Bond Orbitals (Summary): Principal Delocalizations NBO Occupancy Energy (geminal,vicinal,remote) =============================================================================== Molecular unit 1 (O2) 1. BD ( 1) O 1- O 2 1.00000 -1.03224 2. BD ( 2) O 1- O 2 1.00000 -0.45369 3. BD ( 3) O 1- O 2 1.00000 -0.45369 4. CR ( 1) O 1 0.99997 -19.14436 12(v) 5. CR ( 1) O 2 0.99997 -19.14436 8(v) 6. LP ( 1) O 1 0.99984 -0.87950 12(v) 7. LP ( 1) O 2 0.99984 -0.87950 8(v) 8. RY*( 1) O 1 0.00019 0.95747 9. RY*( 2) O 1 0.00000 0.88719 10. RY*( 3) O 1 0.00000 0.88719 11. RY*( 4) O 1 0.00000 1.07773 12. RY*( 1) O 2 0.00019 0.95747 13. RY*( 2) O 2 0.00000 0.88719 14. RY*( 3) O 2 0.00000 0.88719 15. RY*( 4) O 2 0.00000 1.07773 16. BD*( 1) O 1- O 2 0.00000 0.26370 17. BD*( 2) O 1- O 2 0.00000 -0.13403 18. BD*( 3) O 1- O 2 0.00000 -0.13403 ------------------------------- Total Lewis 6.99962 ( 99.9946) Valence non-Lewis 0.00000 ( 0.0000) Rydberg non-Lewis 0.00038 ( 0.0054) ------------------------------- Total unit 1 7.00000 (100.0000) Charge unit 1 1.00000 Ding Xunlei 2003-11-05 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl*at*mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl = = = = = = = = = = = = = = = = = = = =