From chemistry-request@server.ccl.net Fri Mar 16 10:45:52 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GFjqD26488 for ; Fri, 16 Mar 2001 10:45:52 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA75084; Fri, 16 Mar 2001 09:57:57 -0500 (EST) Date: Fri, 16 Mar 2001 09:57:57 -0500 From: Rick Venable To: "J. D. Gans" cc: chemistry@ccl.net Subject: Re: CCL:Qmol: Molecular viewer for Windows In-Reply-To: <3AB12069.9091FDB5@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 15 Mar 2001, J. D. Gans wrote: > Qmol is a OpenGL based program for viewing molecular structures and > animating molecular trajectories. It runs under Windows 95/98/NT/00 and > supports the following features: > > (*) Animate molecular trajectories stored in the DCD file format (both > big- and little-endian). As a long time academic CHARMM user, it was *years* before it became apparent to non-Quanta users that a DCD file was the MSI/Polygen name for a CHARMM binary trajectory file. We always referred to them as "trajectory files", or .trj files, an extension in common usage prior to CHARMm, the commercial variant. I think it would be clearer if your blurb referred to CHARMM/CHARMm explicitly, in addition to file extension that has meaning mostly to Quanta users. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Thu Mar 15 23:46:26 2001 Received: from mta1.263.net ([202.96.44.43]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2G4kPD23435 for ; Thu, 15 Mar 2001 23:46:25 -0500 Received: by mta1.263.net (Postfix, from userid 60001) id EDECB52DB; Fri, 16 Mar 2001 12:46:57 +0800 (CST) MIME-Version: 1.0 Message-Id: <3AB19AC1.20802@mta1> Date: Fri, 16 Mar 2001 12:46:57 +0800 (CST) From: "Fan Jianmiao" To: chemistry@ccl.net Subject: Error of Gaussian 98 Link 1801 X-Priority: 3 X-Originating-IP: [61.132.182.2] Dear CCLers: I had a problem in calculating some small moleculers. The Log file was posted below: " **** Fatal Problem: The largest alpha MO coefficient is 0.12599899D+04 Error termination via Lnk1e in /usr/g98/l801.exe. Job cpu time: 0 days 0 hours 11 minutes 43.1 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 1 Scr= 1" The method I used is : "#p mp2/6-31+g* opt freq opt 0 1 " Can anyone give me some explaination about this error?. Thanks! With My Best Regards, Sincerely yours, Jim Fan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fan Jianmiao(Jim_Fan) Department of Chemistry East Campus,USTC Hefei,Anhui,230026,P.R.China Tel:86-551-3654322(dorm) E-Mail:jim_fan@263.net 86-551-3606640(lab) Http://boc.ustc.edu.cn/jimfan/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _____________________________________________ 35款手机网上最低价 http://shopping.263.net/hotsale/topmobile/ 网上化妆品专卖场 http://shopping.263.net/category04.htm From chemistry-request@server.ccl.net Thu Mar 15 23:54:39 2001 Received: from web13206.mail.yahoo.com ([216.136.174.191]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2G4scD23457 for ; Thu, 15 Mar 2001 23:54:38 -0500 Message-ID: <20010316045354.66012.qmail@web13206.mail.yahoo.com> Received: from [65.6.48.45] by web13206.mail.yahoo.com; Thu, 15 Mar 2001 20:53:54 PST Date: Thu, 15 Mar 2001 20:53:54 -0800 (PST) From: mike smith Subject: Re: CCL:experiment of H-bond strength in solution To: Jordi Villa , chemistry@ccl.net Cc: jsuehnel@imb-jena.de In-Reply-To: <3AB0DF85.9A30AE1E@usc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Thanks a lot to Jordi & others for response! Since Jordi mentioned the EVB theory by Warshel, it reminders me another method by the same group, which is combined QM and Langevin Dipole. In J. Phys. Chem B., 1999, 103, 884, they studied the DNA base pair H-bond and stacking by MP2/LD. They got the potential curves in gas phase and solution for stacking, but not for H-bond. I guess: (1)The H-bond potential curves in solution may be very flat, (2)the error bar of their results could not be small, for example the free energy for many base pairs are almost the same. (3)EVB can't be better than MP2/LD for this problem, otherwise, there should already be resluts published. I just found another paper which is the updated version of the Kollman's work in 1990. It's from R Lavery's group, in J Am Chem Soc, 1999, 121, 9503. Almost same method, same system, but with more advanced computer power & better force field. They gave some surprising results: in the free energy surfaces of AT & CG in solution, there are two minima, and two transition states, instead of normally only one minimum for the dissociation curve. And at the 2nd minimum, the base pairs are separated by about 5.5 A, and it's explained as one water forming a bridge at that distance. One way to confirm the 2nd minimum could be high accuracy QM calculations, with base pair(different distances) plus a few explicit water molecules. J. Phys chem A, 2000, 104, 11177 can be one of the attemps, but the bases are still very close to each other. Hope more results could be available by that group, or higher accuracy simulation by QM/MM with a few explicit water molecules in the QM region. --Mike --- Jordi Villa wrote: > Dear Mike, > > One of the best ways to simulate this is by using > the EVB method by Warshel in, > for example: > > An Empirical Valence Bond Approach for Comparing > Reactions in Solutions and in > Enzymes, A. Warshel and R. M. Weiss, J. Am. Chem. > Soc. 102, 6218 (1980). > Simulation of Enzyme Reactions Using Valence Bond > Force Fields and Other Hybrid > Quantum/Classical Approaches, J. 舚vist and A. > Warshel, Chem. Rev. 93, 2523 > (1993). > > and specifically, on the strength of HB's, a clear > explanation is given in: > > On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, > A. Warshel, A. Papazyan and > P. A. Kollman, Science 269, 102 (1995). > > Also, a simplified version of the use of the EVB for > HB's can be found at > http://www.tanchi.com/tufts/ > > Hope this helps > > Jordi > > > mike smith wrote: > > > Dear all, > > > > Since it's well-known that the H-bond strength > will be > > highly weaken in solution, compared with that in > gap > > phase, I am curious if there is any experimental > > evidence or hint available. > > > > Also, I found two papers on the potential enrgy > curves > > of H-bond in gas-phase and solution: > > (1)Dang, L X; Kollman, P. A, > > J Am Chem Soc, 1990, 112,503 > > > > AT base pair (H-bond & stacking) > > from 12kcal/mol(gas) to 0.8kcal/mol > (solution) > > > > (2)Osapay, K; Young W S; Brooks C L; Case D A > > J Phys Chem 1996, 100, 2698 > > Updated in Annu Rev Phys Chem, 2000, 51, 129 > > > > formamide dimer > > from 6.7 kcal/mol to 0.8 kcal/mol > > > > Here, I am wondering if any of you could provide > me > > more related reference. Also, any discussion on > the > > method to simulate this accurately would be highly > > appreciated. > > > > Thanks for your attention! > > > > --Mike > > > > __________________________________________________ > > Do You Yahoo!? > > Yahoo! Auctions - Buy the things you want at great > prices. > > http://auctions.yahoo.com/ > > > > -- > Jordi Villa i Freixa > jorgevil@usc.edu > http://laetro.usc.edu/wgroup/people/jorgevil > Department of Chemistry, University of Southern > California > Los Angeles, CA, USA, 90089-1062 > Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 > > > __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Fri Mar 16 02:25:14 2001 Received: from vytautas.vdu.lt (mail@[193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2G7P8D23748 for ; Fri, 16 Mar 2001 02:25:10 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 14dobO-0003jm-00; Fri, 16 Mar 2001 09:24:46 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id JAA13659; Fri, 16 Mar 2001 09:24:47 +0200 (GMT) Message-ID: <3AB12531.96293610@vaidila.vdu.lt> Date: Thu, 15 Mar 2001 21:25:21 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Eugene.Leitl@lrz.uni-muenchen.de CC: "Phillip D. Matz" , Yubo Fan , Familia Esguerra Neira , chemistry@ccl.net Subject: Re: CCL:Short Budget References: <006501c0ad7e$404a0050$b4297986@chem.wsu.edu> <3AB13A67.B9476D32@lrz.uni-muenchen.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Good day CCL'ers, The talk turned to something other way from initial topic, so I should some excuse to Yubo Fan. About Athlon and DDR .... Yes, I have surfed internet right for this topic about DDR benchmarks and Athlon. The improvement of DDR to common memory is not very impressive. I think the essence of DDR is very good, as the new efficient PC memory is market will have its place and we all are interested in high speed and in price affordable RAM. The problem about DDR and Athlon could be that AMD started DDR implementation late compared to Intel. There is possibility, that DDR techniques could became more efficient in Athlon (AMD) systems in the future, as good CPU needs good RAM :)). But this is just philosophy ... I would like to ask about dual Athlon motherboards ... Could anyone point to manufacture of dual M/B for Athlon or post the link to pages concerning dual Athlon systems ? Best regards A.Ziemys > Athlons seem to not be able to make much use from DDR SDRAM's higher > bandwidth, but Gaussian98 might be different in this case. It will be > interesting to compare it with Gaussian98 benchmarks on dual-Athlong DDR > systems (a well-known Beowulfer is currently running a few benchmarks, > hopefully it will include Gaussian98). From chemistry-request@server.ccl.net Fri Mar 16 04:40:29 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2G9eSD24160 for ; Fri, 16 Mar 2001 04:40:28 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id KAA13881; Fri, 16 Mar 2001 10:40:28 +0100 (MET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id KAA13014; Fri, 16 Mar 2001 10:23:57 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 16 Mar 01 10:40:27 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 16 Mar 01 10:40:25 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Alexandre Hocquet" , CHEMISTRY@ccl.net Date: Fri, 16 Mar 2001 10:40:14 +0100 Subject: Re: Dirac Citation, reductionism and an advertisement Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Dear Alexandre: > To say that Dirac did NOT claim this, is certainly correct stricto sensu. To > imply that Dirac did not believe in a reductionist approach of chemistry is > another matter. Among the historians of science that interested themselves to > the subject, i cannot think of someone not seeing Dirac as a strong > reductionnist. My comment was meant to emphasize that 'Dirac's dictum', taken at face value, essentially agrees with present day common sense (at least to me). I have allways felt that his statement was misinterpreted. - But what did Dirac "believe"? He died in 1984, 55 years after his 1929 statement. I wonder if he ever commented upon the subject during his later years? I have been told that Dirac was a rather special, eccentric person (complete lack of interest in art and literature), and after the mid-1930s he largely failed to produce any physics of lasting value, emphasizing an idiosyncratic conception of 'mathematical beauty'. So it seems quite likely that he would have adopted a reductionist point of view. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Mar 16 09:57:59 2001 Received: from matavnet.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2GEvwD26114 for ; Fri, 16 Mar 2001 09:57:58 -0500 Received: (qmail 15233 invoked from network); 16 Mar 2001 15:57:56 +0100 Received: from line-140-29.dial.matav.net (HELO cthulhu) (145.236.140.29) by mail.matavnet.hu with SMTP; 16 Mar 2001 15:57:57 +0100 Message-ID: <009501c0ae29$d29bec60$0200a8c0@cthulhu> From: "Tamas Gunda" To: "Zhangxd" , References: Subject: Re: CCL:about sybyl Date: Fri, 16 Mar 2001 16:00:20 +0100 Organization: University of Debrecen 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Xiaodong, Sybyl seemingly has some problem when recognizing the atom types. Could you attach or include me the original pdb file? An atom entry line should look like this: ATOM 1 N ALA 1 0.340 1.018 0.550 The first token should be ATOM in the case of a peptide built from "official" amino acids, and the fourth one the abbrevation of an amino acid. If the line looks like HETATM 1 N UNK 1 0.340 1.018 0.550 then probably the generation of the pdb file was not correct. regards Dr Tamas Gunda Dr Tamas E. Gunda Research for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat > hi, everyone > > I build a small molecule with xleap in AMBER, then save the pdb file, then > use to SYBYL to save mol2 file for the AUTODOCK. But when I use SYBYL (I > am newer for SYBYL) to generate the mol2 file, it says: > > 33 16 36 1 > 34 19 20 2 > 35 19 21 1 > 36 21 37 1 > 37 21 38 1 > 38 21 39 1 @SUBSTRUCTURE > 1 **** 1 TEMP 0 **** **** 0 ROOT > @SET UNK_ATOMS STATIC ATOMS > AMSOM **** Atom types guessed for these atoms 22 1 2 3 4 5 6 7 8 9 10 11 > 12 13 14 15 16 17 18 19 \ > 20 21 22 > > When I used the build/edit in sybyl, I did not find out the error. > > Thank you for your reply and suggestion. > > With best regards, > > xiaodong From chemistry-request@server.ccl.net Fri Mar 16 11:11:33 2001 Received: from mail.iitk.ac.in ([210.212.54.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GGBUD26891 for ; Fri, 16 Mar 2001 11:11:31 -0500 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.2/8.9.2) with ESMTP id JAA02403 for ; Fri, 16 Mar 2001 09:55:54 +0530 (IST) Received: from mailer.cc.iitk.ac.in (IDENT:ranjan@mailer.cc.iitk.ac.in [172.31.1.15]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with ESMTP id JAA03046 for ; Fri, 16 Mar 2001 09:42:02 +0530 (IST) Date: Fri, 16 Mar 2001 09:47:53 +0530 (IST) From: "97104 Chinmoy Ranjan UG(CHM)." X-Sender: ranjan@mailer.cc.iitk.ac.in To: CHEMISTRY@ccl.net Subject: difficulty in using Babel Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All, Its to Babel users. I was try to convert a pdb file to mol2 format using babel but while doing the calculation i get the following message: . . . . atom 8188 is isolated, type=O atom 8189 is isolated, type=O Unable to assign HYB type to atom 1333 type = N Unable to assign HYB type to atom 1334 type = N Unable to assign HYB type to atom 2344 type = N Unable to assign HYB type to atom 3638 type = Mo Unable to assign HYB type to atom 7294 type = Mo The protein molecule(sulphite oxidase) contains Mo at its active site.I donot understand how to get around this problem.Any kind of suggesstion is is appreciated. Thanks in advance. Chinmoy Ranjan CHINMOY RANJAN INDIAN INSTITUTE OF TECHNOLOGY KANPUR From chemistry-request@server.ccl.net Fri Mar 16 11:18:13 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GGIDD26955 for ; Fri, 16 Mar 2001 11:18:13 -0500 Received: from gubookstore.com (gubookstore.com [128.121.230.217]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA21345 for ; Fri, 16 Mar 2001 11:18:11 -0500 (EST) Received: (bprofane@localhost) by gubookstore.com (8.8.8) id WAA97079; Wed, 14 Mar 2001 22:10:36 -0700 (MST) Date: Wed, 14 Mar 2001 22:10:36 -0700 (MST) Message-Id: <200103150510.WAA97079@gubookstore.com> To: chemistry@ccl.net From: coolio@acmemail.net Subject: Tell-a-Friend A true writers website. I stumbled on it, and thought I should forward it on to another writer. They are also giving away a Free Ebook every week. Give it a look. www.greatunpublished.com/writers.htm ======================================================================== This email was generated by "tell-a-friend" at www.greatunpublished.com/writers/tellafriend.htm "Where the Writers Are On Top!" www.greatUNpublished.com If you feel that this system has been abused please contact admin@greatunpublished.com -------------------- This message is the result of a Tell a Friend form at http://www.greatunpublished.com/Writers/tellafriend.htm From chemistry-request@server.ccl.net Fri Mar 16 11:17:32 2001 Received: from mail1.ats.rochester.edu (lozg@[128.151.224.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GGHWD26949 for ; Fri, 16 Mar 2001 11:17:32 -0500 Received: from localhost (lozg@localhost) by mail1.ats.rochester.edu (8.11.1/8.11.1) with ESMTP id f2GGHr95110942 for ; Fri, 16 Mar 2001 11:17:53 -0500 (EST) Date: Fri, 16 Mar 2001 11:17:53 -0500 From: LINGHAO ZHONG X-Sender: lozg@mail1.ats.rochester.edu To: chemistry@ccl.net Subject: docking of cyclic peptide Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all: I am trying to find the optimal binding conformation for a small peptide docking to a protein. Unfortunately the pepetide is a cyclic one, which causes problem in Autodock. The program kept giving me core dump error, which I assumed to be caused by the cyclic conformation of the peptide, and I wanted it to be flexible! I have tried a linear peptide to the same protein, it worked well. Has anyone ever run into the same situation? Is there any novel protocol to deal with the docking of cyclic peptide? Any input will be appreciated! Linghao Zhong ___________________________ Graduate Student Department of Chemistry University of Rochester Rochester, NY 14627-0216 Tel. (716)275-2980 From chemistry-request@server.ccl.net Fri Mar 16 11:26:44 2001 Received: from mail.iitk.ac.in ([210.212.54.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GGQfD26993 for ; Fri, 16 Mar 2001 11:26:41 -0500 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.2/8.9.2) with ESMTP id IAA00054 for ; Thu, 15 Mar 2001 08:31:55 +0530 (IST) Received: from CHINMOY ([172.31.76.193]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with SMTP id IAA22120 for ; Thu, 15 Mar 2001 08:18:06 +0530 (IST) Message-ID: <000a01c0acfb$5403d540$c14c1fac@CHINMOY> From: "chinmoy ranjan" To: Subject: Difficulty while using babel Date: Thu, 15 Mar 2001 08:25:01 +0530 Hello All, While trying to convert a pdb file to mol2 format using babel I get the following message without the job being done. The proytein molecule has Mo at its active site .Could anyone suggest how to get around this problem. Unable to assign HYB type to atom 1333 type = N Unable to assign HYB type to atom 1334 type = N Unable to assign HYB type to atom 2344 type = N Unable to assign HYB type to atom 3638 type = Mo Unable to assign HYB type to atom 7294 type = Mo Thanks CHINMOY RANJAN INDIAN INSTITUTE OF TECHNOLOGY KANPUR From chemistry-request@server.ccl.net Fri Mar 16 11:16:03 2001 Received: from hope.edu ([198.110.98.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GGG3D26936 for ; Fri, 16 Mar 2001 11:16:03 -0500 Received: from [198.110.101.2] (polik@hope.edu); Thu, 15 Mar 2001 11:23:45 -0500 X-WM-Posted-At: hope.edu; Thu, 15 Mar 01 11:23:45 -0500 Message-Id: <4.2.2.20010315110859.049f9260@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Thu, 15 Mar 2001 11:20:12 -0500 To: CHEMISTRY@ccl.net From: "William F. Polik" Subject: Re: CCL:MOPAC software In-Reply-To: <200103151238.NAA24557@alpha.luc.ac.be> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 01:38 PM 3/15/01 +0100, you wrote: >you could take a look at http://www.fqspl.com.pl/winmopac > > >I am very interesting with the MOPAC software, and I would like to ask you > >if there is an available version of MOPAC, please tell me where I could > >obtain it. MOPAC2000 (for various platforms) commercially available as indicated above. The older, public domain, free versions of MOPAC, such as MOPAC6 and MOPAC7 (which is a pre-release version of MOPAC93) are available from the ccl.net software archives at ftp.ccl.net in the /pub/software/chemistry directory and below. In particular, check out /pub/software/chemistry/SOURCES/FORTRAN/mopac6_sources and /pub/software/chemistry/SOURCES/FORTRAN/mopac7_sources Complete installation instructions for MOPAC7 on linux are available at http://www.chem.hope.edu/webmo/support/mopac_linux.html Will Polik =================================================================== William F. Polik email: polik@hope.edu Department of Chemistry url: http://www.chem.hope.edu/~polik Hope College phone: (616) 395-7639 35 East 12th Street fax: (616) 395-7118 Holland, MI 49422-9000 =================================================================== From chemistry-request@server.ccl.net Fri Mar 16 12:24:26 2001 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GHOQD27287 for ; Fri, 16 Mar 2001 12:24:26 -0500 Received: from mail.chem.tamu.edu ([165.91.179.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Fri, 16 Mar 2001 11:24:52 -0600 Message-ID: <3AB24C25.3B2F725C@mail.chem.tamu.edu> Date: Fri, 16 Mar 2001 11:23:49 -0600 From: lakshmi@mail.chem.tamu.edu (Sahasranaman Mahalakshmi) X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: MOLPRO Content-Type: multipart/mixed; boundary="------------41F7E108C5CD68C6C8FBC235" This is a multi-part message in MIME format. --------------41F7E108C5CD68C6C8FBC235 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers, I have been trying to do a MCSCF calculation using molpro. The program gets terminated at RHF-SCF itself. The error message is as follows : PROgram RHF-SCF (open shell) NUmber of electrons: 13+ 10- SPace SYmmetry=2 Spin Symmetry=Quartet COnvergence thresholds: 3.16E-06(Density) 1.00E-07(energy) Max. number of Iterations: 60 Interpolation Type: DIIS Interpolation STEPS: 2(START) 1(STEP) LEVEL SHIFTS: -0.30(closed) 0.00(open) ?ERROR IN GET_INFO: NO DUMP RECORD: 2100.2 The input file is enclosed as an attachment. Please let me know how could I correct the error. Thanking You, Mahalakshmi --------------41F7E108C5CD68C6C8FBC235 Content-Type: text/plain; charset=us-ascii; name="B3N.avdz.optgeom" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="B3N.avdz.optgeom" output=/worklv/lakshmi/B3N/molpro/rhom/b3n.avdz.out KEEP=/worklv/lakshmi/molpro_junk SCR=/worklv/lakshmi/molpro_junk cat <$SCR/z17 ***,b3n memory,8,m file,1,oi.int; file,2,b3n.wfu; geometry={ 4 this is geometry optimization using cartesian B, 0.0000, 0.0000, -1.4140 B, 0.0000, 0.8355, 0.0000 B, 0.0000, -0.8355, 0.0000 N, 0.0000, 0.0000, 1.1286 } basis={ spd,B,AVDZ spd,N,AVDZ} int; PRI,0; rhf occ,8,2,3,0; wf,23,2,3 save,2100.2; orbprint,3; optg multi occ,10,2,4,0; closed,6,1,2,0; optg ! /chem/Molpro/molpro2000.1/bin/molpro -W$KEEP -I$SCR -d$SCR <$SCR/z17 >$output --------------41F7E108C5CD68C6C8FBC235-- From chemistry-request@server.ccl.net Fri Mar 16 15:26:59 2001 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GKQxD28582 for ; Fri, 16 Mar 2001 15:26:59 -0500 Received: from mole.chem.duke.edu (mole.chem.duke.edu [152.3.169.102]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id PAA09654 for ; Fri, 16 Mar 2001 15:27:00 -0500 (EST) Received: from localhost (andres@localhost) by mole.chem.duke.edu (8.9.3+Sun/8.9.3) with ESMTP id PAA03106 for ; Fri, 16 Mar 2001 15:28:43 -0500 (EST) X-Authentication-Warning: mole.chem.duke.edu: andres owned process doing -bs Date: Fri, 16 Mar 2001 15:28:42 -0500 (EST) From: Gerardo Andres Cisneros X-X-Sender: To: Subject: Gaussian on beowulf cluster In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello A couple of weeks ago I posted a message asking for suggestions in getting gaussian to run in parallel on a beowulf cluster. Almost all replys said to update the 2.2.16x kernel. I've upgraded all the nodes to 2.2.17-14 but I still have the same problem. Basically if I run g98 on a single processor the program runs great. I've ran several of the tests that come with g98's distro and the results are the same. However, when I use more than one node, if the job takes a lot of time, invariably one of the slave nodes will run out of memory because g98 will fail to kill the l*.exe processes on the slave nodes so I'll have a bunch of phantom processes just taking up memory on the slave nodes. Here's a small part of the output from using "setenv GAUSS_LFLAGS -vv" with a parallel run in the cluster: > ... ******************************************** node name: rho3 official node name: rho3.chem.duke.edu config lookup name: rho3 executable directory: /usr/local/g98/linda-exe executable name: l701.exel working directory: /usr/execute/pbs debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** node name: rho4 official node name: rho4.chem.duke.edu config lookup name: rho4 executable directory: /usr/local/g98/linda-exe executable name: l701.exel working directory: /usr/execute/pbs debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** node name: rho5 official node name: rho5.chem.duke.edu config lookup name: rho5 executable directory: /usr/local/g98/linda-exe executable name: l701.exel working directory: /usr/execute/pbs debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** node name: rho7 official node name: rho7.chem.duke.edu config lookup name: rho7 executable directory: /usr/local/g98/linda-exe executable name: l701.exel working directory: /usr/execute/pbs debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** ntsnet: starting master process on rho8.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_sh /usr/local/g98/linda-exe/l701.exel 0 reactrho2.chk 1 /usr/execute/pbs/scrdir/Gau-19346.int 0 /usr/execute/pbs/scrdir/Gau-19346.rwf 0 /usr/execute/pbs/scrdir/Gau-19346.d2e 0 /usr/execute/pbs/scrdir/Gau-19346.scr 0 /usr/execute/pbs/scrdir/Gau-19345.inp 0 junk.out 0 +LARGS -kainterval 1000 -master 18469 -tsnetport 22308 -maxworkers 5 -minworkers 5 -minwait 600 -maxwait 600 -nodename rho8.chem.duke.edu -kaon ntsnet: starting 1 worker on rho2.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho2.chem.duke.edu -r rsh /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 1 -nodename rho2.chem.duke.edu ntsnet: starting 1 worker on rho3.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho3.chem.duke.edu -r rsh /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 2 -nodename rho3.chem.duke.edu ntsnet: starting 1 worker on rho4.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho4.chem.duke.edu -r rsh /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 3 -nodename rho4.chem.duke.edu ntsnet: starting 1 worker on rho5.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho5.chem.duke.edu -r rsh /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 4 -nodename rho5.chem.duke.edu ntsnet: starting 1 worker on rho7.chem.duke.edu /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho7.chem.duke.edu -r rsh /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 5 -nodename rho7.chem.duke.edu ntsnet: waiting for linda group message ntsnet: received linda group message: group has 6 members malloc failed.: Cannot allocate memory ntsnet: worker on node rho3.chem.duke.edu exited abnormally ntsnet: beginning to shutdown remote processes Killed by signal 15. Killed by signal 15. Killed by signal 15. Killed by signal 15. ntsnet: shutting down with return code 143 [1] + Exit 1 g98l react6p 823.210u 95.200s 19:14.68 79.5% 0+0k 0+0io 397099pf+6w > Even though the console output says it shuts down remote processes by signal 15 it really doesn't. react6p is a QST3 caculation using HF/3-21G* that running on a single processor alpha took 32 minutes (local test). Has anybody had a similar problem?. Thanks in advance, Andres -- G. Andres Cisneros Department of Chemistry Duke University andres@chem.duke.edu From chemistry-request@server.ccl.net Fri Mar 16 15:32:22 2001 Received: from Post-Office.UH.EDU ([129.7.1.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GKWMD28640 for ; Fri, 16 Mar 2001 15:32:22 -0500 Received: from CONVERSION-DAEMON by Post-Office.UH.EDU (PMDF V5.2-32 #40812) id <0GAB0060151OK3@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Fri, 16 Mar 2001 14:32:18 -0600 (CST) Received: from uh.edu (Kroll.BCHS.UH.EDU [129.7.2.217]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0GAB002LD51MQV@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Fri, 16 Mar 2001 14:32:11 -0600 (CST) Date: Fri, 16 Mar 2001 14:29:47 -0600 From: Hung-Chung Huang Subject: Eigenvectors and eigenvalues! To: CHEMISTRY@ccl.net Cc: HCHuang@UH.EDU Message-id: <3AB277BB.7010406@uh.edu> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; m18) Gecko/20001108 Netscape6/6.0 X-Accept-Language: en,pdf Dear CCLers, I want to do some essential dynamics analysis for my protein from MD simulations by NAMD2.2. This analysis will be like the one described in the paper by Berendsen et al. (Title: Essential Dynamics of Proteins, Journal: PROTEINS: Structure, Function, and Genetics 17:412-425, 1993); therefore, I need to calculate the eigenvectors and eigenvalues for my system. So, can somebody give me some clues about how to do this kind of calculations for protein systems? Also, I am basically using VMD for the analyses of my MD data. Does anybody know if there is a way for VMD to do this kind of calculations? Your hints and suggestions will be much appreciated! Joe -- http://adrik.bchs.uh.edu/~jhuang From chemistry-request@server.ccl.net Fri Mar 16 18:22:44 2001 Received: from jaguar.it.wsu.edu (root@[134.121.0.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2GNMhD29446 for ; Fri, 16 Mar 2001 18:22:43 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id PAA32076; Fri, 16 Mar 2001 15:22:42 -0800 (PST) Message-ID: <001501c0ae6f$fffa23c0$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Gerardo Andres Cisneros" , References: Subject: Re: CCL:Gaussian on beowulf cluster Date: Fri, 16 Mar 2001 15:22:42 -0800 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 Hello Andres, Curious. I run G98 + Linda + RH6.2 with the 2.2.16-3 kernel without these errors, so maybe I could try your particular input file and see if I can reproduce the error you are getting. I do not understand why your particular installation of G98 + Linda is failing to kill the l*.exel processes on the slave nodes, I haven't experienced this yet. Maybe you should ask the Beowulf listers if they have come across this error with G98L on their clusters. I have experienced the particular error that you see at the end of your output file ( malloc failed.: Cannot allocate memory) but I doubt my problem is related to yours. My problem turned out to be an improper (i.e. none ;) ) grounding of my network card and motherboard which would gradually lead up to the point that enough static electricity would gather on the network card to cause the computer to hang - yeah I know, not a good thing... But your problem sounds like a software issue (my personal opinion with absolutely no technical merit). Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Gerardo Andres Cisneros" To: Sent: Friday, March 16, 2001 12:28 PM Subject: CCL:Gaussian on beowulf cluster > > Hello > > A couple of weeks ago I posted a message asking for suggestions in getting > gaussian to run in parallel on a beowulf cluster. Almost all replys > said to update the 2.2.16x kernel. I've upgraded all the nodes to > 2.2.17-14 but I still have the same problem. > > Basically if I run g98 on a single processor the program runs great. I've > ran several of the tests that come with g98's distro and the results are > the same. > > However, when I use more than one node, if the job takes a lot of time, > invariably one of the slave nodes will run out of memory because g98 will > fail to kill the l*.exe processes on the slave nodes so I'll have a bunch > of phantom processes just taking up memory on the slave nodes. > > Here's a small part of the output from using "setenv GAUSS_LFLAGS -vv" > with a parallel run in the cluster: > > > > >... > ******************************************** > node name: rho3 > official node name: rho3.chem.duke.edu > config lookup name: rho3 > executable directory: /usr/local/g98/linda-exe > executable name: l701.exel > working directory: /usr/execute/pbs > debugger: > linda rsh argument: rsh > linda rcp argument: > user: > adjusted load: 1.000000 > threshold: 20.000000 > speedfactor: 1.000000 > available: True > nice: False > master: False > processes scheduled: 1 > maximum processes: 1 > ******************************************** > node name: rho4 > official node name: rho4.chem.duke.edu > config lookup name: rho4 > executable directory: /usr/local/g98/linda-exe > executable name: l701.exel > working directory: /usr/execute/pbs > debugger: > linda rsh argument: rsh > linda rcp argument: > user: > adjusted load: 1.000000 > threshold: 20.000000 > speedfactor: 1.000000 > available: True > nice: False > master: False > processes scheduled: 1 > maximum processes: 1 > ******************************************** > node name: rho5 > official node name: rho5.chem.duke.edu > config lookup name: rho5 > executable directory: /usr/local/g98/linda-exe > executable name: l701.exel > working directory: /usr/execute/pbs > debugger: > linda rsh argument: rsh > linda rcp argument: > user: > adjusted load: 1.000000 > threshold: 20.000000 > speedfactor: 1.000000 > available: True > nice: False > master: False > processes scheduled: 1 > maximum processes: 1 > ******************************************** > node name: rho7 > official node name: rho7.chem.duke.edu > config lookup name: rho7 > executable directory: /usr/local/g98/linda-exe > executable name: l701.exel > working directory: /usr/execute/pbs > debugger: > linda rsh argument: rsh > linda rcp argument: > user: > adjusted load: 1.000000 > threshold: 20.000000 > speedfactor: 1.000000 > available: True > nice: False > master: False > processes scheduled: 1 > maximum processes: 1 > ******************************************** > ntsnet: starting master process on rho8.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_sh > /usr/local/g98/linda-exe/l701.exel 0 reactrho2.chk 1 > /usr/execute/pbs/scrdir/Gau-19346.int 0 > /usr/execute/pbs/scrdir/Gau-19346.rwf 0 > /usr/execute/pbs/scrdir/Gau-19346.d2e 0 > /usr/execute/pbs/scrdir/Gau-19346.scr 0 > /usr/execute/pbs/scrdir/Gau-19345.inp 0 junk.out 0 +LARGS -kainterval 1000 > -master 18469 -tsnetport 22308 -maxworkers 5 -minworkers 5 -minwait 600 > -maxwait 600 -nodename rho8.chem.duke.edu -kaon > ntsnet: starting 1 worker on rho2.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho2.chem.duke.edu -r rsh > /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker > rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 1 -nodename > rho2.chem.duke.edu > ntsnet: starting 1 worker on rho3.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho3.chem.duke.edu -r rsh > /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker > rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 2 -nodename > rho3.chem.duke.edu > ntsnet: starting 1 worker on rho4.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho4.chem.duke.edu -r rsh > /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker > rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 3 -nodename > rho4.chem.duke.edu > ntsnet: starting 1 worker on rho5.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho5.chem.duke.edu -r rsh > /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker > rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 4 -nodename > rho5.chem.duke.edu > ntsnet: starting 1 worker on rho7.chem.duke.edu > /usr/sca/linda-5.0rh6.0/linux-2.2/bin/linda_rsh rho7.chem.duke.edu -r rsh > /usr/local/g98/linda-exe/l701.exel +LARGS -chdir /usr/execute/pbs -worker > rho8.chem.duke.edu:18469 -workerwait 900 -tsnetref 5 -nodename > rho7.chem.duke.edu > ntsnet: waiting for linda group message > ntsnet: received linda group message: group has 6 members > malloc failed.: Cannot allocate memory > ntsnet: worker on node rho3.chem.duke.edu exited abnormally > ntsnet: beginning to shutdown remote processes > Killed by signal 15. > Killed by signal 15. > Killed by signal 15. > Killed by signal 15. > ntsnet: shutting down with return code 143 > > [1] + Exit 1 g98l react6p > 823.210u 95.200s 19:14.68 79.5% 0+0k 0+0io 397099pf+6w > > > > Even though the console output says it shuts down remote processes by > signal 15 it really doesn't. > > react6p is a QST3 caculation using HF/3-21G* that running on a single > processor alpha took 32 minutes (local test). > > Has anybody had a similar problem?. > > Thanks in advance, > > Andres > > -- > G. Andres Cisneros > Department of Chemistry > Duke University > andres@chem.duke.edu > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Mar 16 23:26:07 2001 Received: from schrodinger.com (root@[192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2H4K6D30253 for ; Fri, 16 Mar 2001 23:20:06 -0500 Received: from schrodinger.com (natasha.schrodinger.com [192.156.98.136]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id OAA27421; Fri, 16 Mar 2001 14:36:04 -0800 Message-ID: <3AB294D8.CA8CC62D@schrodinger.com> Date: Fri, 16 Mar 2001 14:34:00 -0800 From: George Vacek Organization: Schrodinger, Inc. X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "William F. Polik" CC: CHEMISTRY@ccl.net Subject: Re: CCL:MOPAC software References: <4.2.2.20010315110859.049f9260@webmail.hope.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "William F. Polik" wrote: > >you could take a look at http://www.fqspl.com.pl/winmopac > > MOPAC2000 (for various platforms) commercially available as indicated above. Actually, that's WinMopac indicated above, including Mopac97. For Mopac2000 try http://www.schrodinger.com/mopac2.html. The page contains links to regional distributors. Regards, George Vacek =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- vacek@schrodinger.com (503)299-1150 http://www.schrodinger.com/~vacek/ Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 Every culture that has lost myth has lost, by the same token, its natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-