From chemistry-request@server.ccl.net Fri Feb 22 01:55:00 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1M6sx524306 for ; Fri, 22 Feb 2002 01:55:00 -0500 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id g1M6saU13140; Thu, 21 Feb 2002 22:54:36 -0800 Date: Thu, 21 Feb 2002 22:54:36 -0800 (PST) From: Roy Jensen To: chemistry@ccl.net cc: help@gaussian.com Subject: Large H-bonded complexes; freezing and activating coordinates; ONIOM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII All I am trying to look at hydrogen bonding in large complexes with G98. I currently optimize the entire complex with AM1 and then use a higher method on the atoms involved in hydrogen bonding. I am having problems with the latter. I want to freeze all the atoms (no problem with this step) and then selectively activate the desired atomic positions, bond lengths, angles, and dihedral angles. A ONIOM calculation on the final complex should optimize the atoms involved in hydrogen bonding at a higher level while leaving the remaining complex frozen at the AM1 level. Freezing is accomplished with * F * * F * * * F * * * * F Specific atoms, bond lengths, angles, and dihedrals are activated (in the same modredundant block) with 2 A 4 A 2 * A 4 * A * 2 * A * 4 * A * 2 4 * A assuming atoms 2 and 4 need to be activated. The output file shows that the appropriate parameters are being optimized. The problem is that the job completes all steps and the final geometry is IDENTICAL to the input geometry! I am guessing that some unprinted bond lengths, angles, and dihedrals are still frozen, preventing motion of these atoms. I have tried removing (R) and killing (K) all the parameters instead of freezing (F) them. Both of these fail immediately with an 'Incomplete coordinate system.' error. Any suggestions would be appreciated. Is there another way to go about this? Roy Jensen From chemistry-request@server.ccl.net Fri Feb 22 07:35:16 2002 Received: from prserv.net ([32.97.166.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1MCZF500623 for ; Fri, 22 Feb 2002 07:35:16 -0500 Received: from attglobal.net (slip-12-64-6-219.mis.prserv.net[12.64.6.219]) by prserv.net (out2) with SMTP id <2002022212345220203l6ov2e>; Fri, 22 Feb 2002 12:34:53 +0000 Message-ID: <3C75F7CB.ADCCE95@attglobal.net> Date: Fri, 22 Feb 2002 07:48:28 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.73 [en]C-CCK-MCD NSCPCD473 (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Linux Compilers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, Would there likely be incompatabilities between libraries [BLAS and ATLAS] built under RH6.2 [fortran], and object code compiled using RH7.1 [fortran] that wants to use the RH6.2 libraries? Thanks.. John McKelvey From chemistry-request@server.ccl.net Fri Feb 22 06:28:33 2002 Received: from spark1.chem.ut.ee ([193.40.7.91]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g1MBSW531486 for ; Fri, 22 Feb 2002 06:28:32 -0500 Received: (qmail 4632 invoked by uid 502); 22 Feb 2002 11:27:20 -0000 Date: Fri, 22 Feb 2002 13:27:20 +0200 From: Uko Maran To: CHEMISTRY@ccl.net Subject: POSTDOCTORAL POSITIONS ON MOLECULAR MODELING Message-ID: <20020222132719.A4601@theor.chem.ut.ee> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i ----- Forwarded message from Mati Karelson ----- Date: Mon, 18 Feb 2002 13:29:56 +0200 From: Mati Karelson To: uko@chem.ut.ee Subject: Imagetox POSTDOCTORAL POSITIONS ON MOLECULAR MODELING AVAILABLE AT THE UNIVERSITY OF TARTU Applications are invited from young researchers with an interest in joining a four-year (2001-2004) EU network project aimed at the development of models to predict toxicity. The project is titled as "Intelligent Modelling Algorithms for the General Evaluation of TOXicities" (IMAGETOX). The network consists of 7 European laboratories (see the homepage: http://airlab.elet.polimi.it/imagetox/) working in toxicology, computational chemistry and computer science. Grants for 2 post-doctoral positions (up to 20 months) are available to work within this network at the University of Tartu, Estonia (Professor M. Karelson). The grant amount will be 2400 Euro/month for a post-doctoral associate. The post-doc positions require that the candidate holds (or is near to obtain) a PhD. The researcher must be 35 years old or less at the time of his appointment (allowances are possible for special cases). The applicant must be a national of a Member State of the European Community or of an Associated State or have resided in the European Community for at least five years prior to his appointment. Interested candidates should send an application (including CV, summary of research interests and contact information) to: Professor Dr. Mati Karelson Director Centre of Strategic Competence University of Tartu 2 Jakobi Street, Tartu 51014 ESTONIA Fax: +372-7-375264 Email: mati@chem.ut.ee Visit the homepage of the project for the general information http://airlab.elet.polimi.it/imagetox/ ----- End forwarded message ----- From chemistry-request@server.ccl.net Thu Feb 21 21:11:06 2002 Received: from outmail-1.caramail.com ([213.193.12.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1M2AZ517211 for ; Thu, 21 Feb 2002 21:11:05 -0500 Date: Thu, 21 Feb 2002 21:11:05 -0500 Received: from lycos.co.uk (newwww-27.caramail.com [213.193.12.37]) by outmail-1.caramail.com (8.8.8/8.8.8) with SMTP id DAA05119 for chemistry@ccl.net; Fri, 22 Feb 2002 03:10:09 +0100 (MET) Posted-Date: Fri, 22 Feb 2002 03:10:09 +0100 (MET) From: JOSE Drive To: chemistry@ccl.net Message-ID: <1014343808027247@lycos.co.uk> X-Mailer: Caramail - www.caramail.com X-Originating-IP: [213.1.45.6] Mime-Version: 1.0 Subject: RE: autodock Content-Type: multipart/mixed; boundary="=_NextPart_Caramail_0272471014343808_ID" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --=_NextPart_Caramail_0272471014343808_ID Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear colleagues, Many thanks for your replies to my e-mail I have managed to compile nearly all the files except protonate and autodock even after following the HOWto information provided in one of the replies. In the case of protonate I get the following reply on running the make script f77 -c_ protonate _f make: f77: command not found. Make: xxx{protonate.o} Error 127. In the case of autodock ige gcc -DHPPA -DNDEBUG -03 -c -DWRITEPDQSTATE main cc gcc: unrecognised option '-03' main.cc:3:iostreamh:nosuch file or directory In file included from support. h:20 from gs.h:10 from hybrids:h:14 from main cc:6 rep.h:16;iostream h: no file or directory make: xxx{main 0}Error 1. Any suggestions wellcomed Many thanks Claudius D'silva ______________________________________________________ Free Email - http://www.lycos.co.uk Get your domain for =A39.90 - http://lycos.uk.domainnames.com/default.asp?caller=3Dlycos_ef Win a widescreen TV - http://sundayleague.lycos.co.uk --=_NextPart_Caramail_0272471014343808_ID-- From chemistry-request@server.ccl.net Fri Feb 22 21:42:51 2002 Received: from mail8.wlv.netzero.net ([209.247.163.58]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g1N2go525109 for ; Fri, 22 Feb 2002 21:42:51 -0500 Received: (qmail 17951 invoked from network); 23 Feb 2002 02:42:25 -0000 Received: from 1cust217.tnt2.lafayette2.in.da.uu.net (HELO pavilion) (63.25.200.217) by mail8.wlv.netzero.net with SMTP; 23 Feb 2002 02:42:25 -0000 Message-ID: <001601c1bc15$292043c0$0200a8c0@pavilion> From: "jfbaker" To: Subject: problems recompiling AutoDock3 with more gridpoints Date: Fri, 22 Feb 2002 21:52:38 -0500 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 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCLers, We're trying to recompile both AutoGrid and AutoDock to accept a maximum number of 211 grid points, instead of 128. Changing MAX_GRID_PTS to 211 in the 'autocomm.cc' file works just fine for AutoGrid, but doing the same thing for AutoDock produces an executable which quickly segfaults, producing a "virtual memory exceeded in 'new'" message buried in the coredump. Has anyone else run into this problem, and figured out a solution? Any help would be much appreciated! Sincerely, Jerry Baker jfbaker@netzero.net ---------------------------------------------------- Sign Up for NetZero Platinum Today Only $9.95 per month! http://my.netzero.net/s/signup?r=platinum&refcd=PT97 From chemistry-request@server.ccl.net Fri Feb 22 15:20:28 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1MKKS511138 for ; Fri, 22 Feb 2002 15:20:28 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g1MKK5700799 for ; Fri, 22 Feb 2002 14:20:05 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g1MKK5j28908 for ; Fri, 22 Feb 2002 14:20:05 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 22 Feb 2002 14:20:05 -0600 (CST) From: Jim Phillips To: chemistry@ccl.net Subject: NAMD 2.4b2 (Parallel MD) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.4b2 Release Announcement | | | +--------------------------------------------------------------------+ February 22, 2002 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.4b2 has several advantages over NAMD 2.3: - Greatly improved parallel scaling with particle mesh Ewald. - Locally enhanced sampling via multiple non-interacting images. - Alchemical free energy perturbation for mutation, ligands, etc. - GROMACS ASCII topology and coordinate input file compatibility. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. "Biomedical Applications of Molecular Dynamics on the TeraGrid", a three-day NAMD users workshop co-sponsored by NCSA, will be held April 17-19 in Urbana, Ilinois and broadcast on the Access Grid. See http://www.ncsa.uiuc.edu/Divisions/eot/training/NAMD/ for more information. The deadline for registration is March 7, 2002. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Fri Feb 22 16:42:15 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1MLfi512214 for ; Fri, 22 Feb 2002 16:42:14 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16eNOL-0005B0-00; Fri, 22 Feb 2002 21:38:09 +0000 Date: Fri, 22 Feb 2002 21:38:09 +0000 (GMT) From: Szilveszter Juhos To: jmmckel@attglobal.net cc: chemistry@ccl.net Subject: Re: CCL:Linux Compilers In-Reply-To: <3C75F7CB.ADCCE95@attglobal.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 22 Feb 2002 jmmckel@attglobal.net wrote: > Would there likely be incompatabilities between libraries [BLAS and > ATLAS] built under RH6.2 [fortran], and object code compiled using RH7.1 > [fortran] that wants to use the RH6.2 libraries? Likely. Try to install the "compat" rpm-s (compat-libstdc++-6.2-2.9.0.9 compat-glibc-6.2-2.1.3.2 for 7.0 something similar should be for 7.1) also you can check dynamic lib dependencies with ldd. Hope it helps: Szilva From chemistry-request@server.ccl.net Fri Feb 22 17:20:54 2002 Received: from smtp02.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1MMKr512778 for ; Fri, 22 Feb 2002 17:20:54 -0500 Received: from pak3 (unknown [140.232.202.93]) by smtp02.sohu.com (Postfix) with ESMTP id 0EB896A9A0 for ; Sat, 23 Feb 2002 06:20:26 +0800 (CST) Message-ID: <007a01c1bbee$eed19e10$5dcae88c@pak3> From: "Alan Leo" To: References: <3C74CAAC.AF2B806F@dcu.ie> Subject: How to calculate BDF(backbone dihedral fluctuations) per residue via Amber? Date: Fri, 22 Feb 2002 17:18:59 -0500 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hi, Do someone know how to calculate BDF(backbone dihedral fluctuations) per residue via Amber? Any tips is much appreciated! Best, Alan