From chemistry-request@server.ccl.net Fri Oct 26 03:20:37 2001 Received: from c0mailgw13.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9Q7KaB12778 for ; Fri, 26 Oct 2001 03:20:37 -0400 Received: from c0web108 (216.163.180.10) by c0mailgw13.prontomail.com (NPlex 5.5.029) id 3BD60BFE000620C3 for chemistry@ccl.net; Fri, 26 Oct 2001 00:16:39 -0700 From: "markus mayer" Message-Id: Date: Fri, 26 Oct 2001 00:16:39 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: Intrepretation of ELF functions etc. X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear Collegue, I have calculated the CaSO4 ELF functions. The plot shows that the value of the function peaks at oxygen (0.8), with almost zero at Ca and little at S. The isosurface is almost spherical at the oxygen atoms, no aggregation of the ELF at the "S-O bond". I have tested something like NaAlH4 in which basically the situation is the same (ELF concentrated at H and is spherical). I have also plotted the electron density instead of the ELF, the situation is consistent with that of ELF. For this compounds, is the X-ray diffraction also look like that? How can I intreprete these diagrams? thanks in advance bjoen ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Fri Oct 26 07:43:12 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QBh6B18756 for ; Fri, 26 Oct 2001 07:43:08 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15x5Qx-0006rK-00; Fri, 26 Oct 2001 13:45:55 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id OAA17143 for ; Fri, 26 Oct 2001 14:23:39 +0200 (GMT) Date: Fri, 26 Oct 2001 14:45:55 +0300 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <216794208.20011026144555@vaidila.vdu.lt> To: CCL Subject: CCL: BSA 3D structure - does anybody knows aby hook ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am searching for BSA - Bovine Serum Albumin - tertiary structure. I surfed www, icuding PDB www database, and it was without any results. ( Here is the last tray .... ) Coul anybody point to any reference about the experimental tertiary structure of BSA ? Bets regards to all Arturas Z. From chemistry-request@server.ccl.net Fri Oct 26 14:41:39 2001 Received: from Mercury.acs.unt.edu ([129.120.220.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QIfcB29269 for ; Fri, 26 Oct 2001 14:41:38 -0400 Received: from iatro.unt.edu (iatro.unt.edu [129.120.48.55]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id NAA16099 for ; Fri, 26 Oct 2001 13:44:33 -0500 (CDT) Received: from gwia.unt.edu (gwia.unt.edu [129.120.48.1]) by iatro.unt.edu (8.9.3/8.9.3) with SMTP id NAA14611 for ; Fri, 26 Oct 2001 13:43:24 -0500 Received: from SMTP-Message_Server by gwia.unt.edu with Novell_GroupWise; Fri, 26 Oct 2001 13:43:18 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 5.5.5.1 Date: Fri, 26 Oct 2001 13:43:01 -0500 From: "Angela Wilson" To: Subject: 02.04.07 Electron Correlation Methodology - COMP/PHYS - National ACS Meeting Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Meeting: National Meeting of the American Chemical Society Time: April 7-11, 2002 Location: Orlando, Florida - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SYMPOSIUM: Recent Advances in Electron Correlation Methodology - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Co-sponsored by the Division of Computers in Chemistry and the Division of Physical Chemistry SUBMISSITION DEADLINE: November 12, 2001 This symposium will bring together researchers from across the world to assess recent progress in the field of electron correlation methodology, including developments in ab initio and density functional theory methodology, as well as important issues related to computational scaling and achieving high accuracy. To date, a tentative list of speakers includes: Rodney Bartlett Axel Becke Daniel Crawford Thom H. Dunning, Jr. Peter Gill Mark Gordon Robert Harrison Martin Head-Gordon Katharine Hunt Poul Jorgensen Wim Klopper Anna Krylov Jan Martin Keiji Morokuma Marcel Nooijen John Perdew George Petersson Piotr Piecuch Peter Pulay Krishnan Raghavachari Dennis Salahub David Sherrill John Stanton Peter Taylor Donald Truhlar - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Abstracts can be submitted for this session on-line at http://oasys.acs.org/. The deadline for abstract submission is NOVEMBER 12, 2002. Particular topics of interest include: development of new density functionals, scaling issues in ab initio correlated methods, new hybrid methods for large chemical systems, basis set methodology, multireference electronic structure approaches, and high accuracy ab initio approaches. Thank you, Angela Wilson University of North Texas Department of Chemistry Box 305070 Denton, Texas 76203-5070 E-mail: akwilson@unt.edu Phone: (940) 565-4296 Fax: (940) 565-4318 From chemistry-request@server.ccl.net Fri Oct 26 11:47:22 2001 Received: from matematicas.udea.edu.co (IDENT:root@[200.24.16.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QFlLB25417 for ; Fri, 26 Oct 2001 11:47:21 -0400 Received: from Debug (IDENT:apache@huitoto.udea.edu.co [200.24.20.158]) by matematicas.udea.edu.co (8.11.2/8.11.2) with SMTP id f9QFkw822894 for ; Fri, 26 Oct 2001 10:46:58 -0500 Message-Id: <200110261546.f9QFkw822894@matematicas.udea.edu.co> To: chemistry@ccl.net From: elfy04@matematicas.udea.edu.co Subject: Gaussin intallation Date: Fri, 26 Oct 2001 15:50:22 GMT X-Mailer: Endymion MailMan Standard Edition v3.0.25 hello cclers: I would like to know if someone has expirence on gaussian compilation on a Red Hat 7.0 pentium IV machine. In particular, I would like to know what kind of Blas library do I have to use. I have used the blas-f2c.a and the linux Single processor BLAS for Pentium II Xeon Version 1.2F. Unfortunatelly, the compilation process ends with an error. Might you please give me a hint? Thanks in advance, Elizebeth Flores Ph.D student. --------------------------------------------------------- La Universidad está en cada uno de nosotros. http://www.udea.edu.co --------------------------------------------------------- Este mensaje fue enviado utilizando "Endymion MailMan". http://www.endymion.com/products/mailman/ From chemistry-request@server.ccl.net Fri Oct 26 07:38:43 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QBcZB18606 for ; Fri, 26 Oct 2001 07:38:38 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 15x5MN-0006r6-00; Fri, 26 Oct 2001 13:41:11 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id OAA17114; Fri, 26 Oct 2001 14:18:55 +0200 (GMT) Date: Fri, 26 Oct 2001 14:41:11 +0300 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <10516509799.20011026144111@vaidila.vdu.lt> To: CCL CC: Arthur Olson , David Goodsell Subject: CCL: AutoDock 3.0.5 - custom constants in code ... In-reply-To: <4.1.20011019160508.00a91280@140.239.39.130> References: <4.1.20011019160508.00a91280@140.239.39.130> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers and Autodock authors, I tried to compile AD 3.0.5 code with common constants and global variables. It goes well. But I wanted to enlarge the maximum number of grid points. By default it was 128. If I try to enlarge it - the compilation do not succeed. How to enlarge the number of grid points ??? What other changes should be applied along ? With best regards Arturas Z. From chemistry-request@server.ccl.net Fri Oct 26 11:54:05 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QFs2B25677 for ; Fri, 26 Oct 2001 11:54:03 -0400 Received: from ppp-212.56.193.92.mldnet.com (ppp-212.56.193.92.mldnet.com [212.56.193.92]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id SAA09716 for ; Fri, 26 Oct 2001 18:56:47 +0300 Date: Fri, 26 Oct 2001 19:04:14 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <1115040472.20011026190414@yahoo.com> To: chemistry@ccl.net Subject: free C/C++ compiller for Win32 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, I am looking for a free C/C++ compiller for Win32 environment. DJGPP is good but only for DOS. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Fri Oct 26 15:24:31 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QJOVB30480 for ; Fri, 26 Oct 2001 15:24:31 -0400 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 f9QJRNa21150; Fri, 26 Oct 2001 14:27:23 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.3+Sun/8.9.1) with ESMTP id OAA27652; Fri, 26 Oct 2001 14:27:22 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 26 Oct 2001 14:27:22 -0500 (CDT) From: Jim Phillips To: Max Valdez cc: Computational Chemistry List Subject: Re: CCL:NAMD analysis tools In-Reply-To: <3BD892AA.ECDE748C@correo.fc.uaem.mx> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII See http://www.ks.uiuc.edu/Research/namd/utilities/ and http://www.ks.uiuc.edu/Development/MDTools/ The namdplot script lets you plot energies in xmgr and you can do some analysis in VMD. -Jim On Thu, 25 Oct 2001, Max Valdez wrote: > Hi CCL'rs > > I'm a newbie to NAMD-VMD or anything related to molecular dynamics, reading the > user guide I could not find any tool to analyse velocities, energies or > anything else from the ouput files, since they are binary, i cannot find a way > to translate them to a xmgr or gnuplot format to read them. Is there anything > obious I'm not seeing? > > Whis tool do the NAMD users use ?. I'm interested on free programs. I'm > learning gromacs too, and it does have that kind of tools, i think there must > be something for NAMD > > Thanks in advance, I will sumarize if it worths for the newbies like me > > Max > > > -= 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 Oct 26 16:09:02 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QK91B31309 for ; Fri, 26 Oct 2001 16:09:01 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA06277; Fri, 26 Oct 2001 15:59:08 -0400 (EDT) Date: Fri, 26 Oct 2001 15:59:08 -0400 From: Rick Venable To: elfy04@matematicas.udea.edu.co cc: chemistry@ccl.net Subject: Re: CCL:Gaussin intallation In-Reply-To: <200110261546.f9QFkw822894@matematicas.udea.edu.co> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 26 Oct 2001 elfy04@matematicas.udea.edu.co wrote: > I would like to know if someone has expirence on gaussian > compilation on a Red Hat 7.0 pentium IV machine. In particular, I > would like to know what kind of Blas library do I have to use. I > have used the blas-f2c.a and the linux Single processor BLAS for > Pentium II Xeon Version 1.2F. Unfortunatelly, the compilation > process ends with an error. > > Might you please give me a hint? It is my understanding that RedHat 7.0 was released with a broken Fortran compiler, and that the problem can be fixed by upgrading either the Fortran compiler alone, or going to RedHat 7.1 It is possible that may be your problem, rather than your choice of BLAS libraries. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 Fri Oct 26 16:37:34 2001 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QKbYB31887 for ; Fri, 26 Oct 2001 16:37:34 -0400 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GLTYRJ00.CS5 for ; Fri, 26 Oct 2001 16:40:32 -0400 Message-ID: <3BD9CA8C.9967311C@umbi.umd.edu> Date: Fri, 26 Oct 2001 16:41:48 -0400 From: "Michael K. Gilson" X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: HYBRID multiple-site titration code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Since someone just asked me about access to the HYBRID titration code*, I went ahead and made it available for download at gilsonlab.umbi.umd.edu. Note that it doesn't compute electrostatic energies, just titration curves and so on based upon these energies. It's free for academic or personal use. Regards, Mike * M. K. Gilson, "Multiple-site titration and molecular modelling: Two Rapid Methods for Computing Energies and Forces for Ionizable Groups in Proteins", Proteins:Struct. Func. Gen.,15:266 - 282, 1993 From chemistry-request@server.ccl.net Fri Oct 26 16:22:36 2001 Received: from mail.ncifcrf.gov ([129.43.100.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9QKMZB31638 for ; Fri, 26 Oct 2001 16:22:35 -0400 Received: from 661301 ([129.43.27.150]) by mail.ncifcrf.gov (8.11.3/8.11.3) with SMTP id f9QKPOJ03322; Fri, 26 Oct 2001 16:25:24 -0400 (EDT) Message-ID: <002b01c15e5c$98ac10a0$961b2b81@661301> From: "Yun Tang" To: "Mike Peleah" , References: <1115040472.20011026190414@yahoo.com> Subject: Re: CCL:free C/C++ compiller for Win32 Date: Fri, 26 Oct 2001 16:27:13 -0400 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 Mike, I would recommend LCC-win32, it works well in win32 environment. Please visit the website for details: http://www.cs.virginia.edu/~lcc-win32/ Best regards, Yun ******************************************************************* * Yun TANG, Ph.D. * * Laboratory of Medicinal Chemistry Tel: 301-846-5974 (O) * * Center for Cancer Research * * National Cancer Institute, NIH * * 376 Boyles Street Fax: 301-846-6033 * * Frederick, MD 21702 E-Mail: yuntang@ncifcrf.gov * ******************************************************************* ----- Original Message ----- From: "Mike Peleah" To: Sent: Friday, October 26, 2001 12:04 PM Subject: CCL:free C/C++ compiller for Win32 > Dear chemistry, > > I am looking for a free C/C++ compiller for Win32 environment. > DJGPP is good but only for DOS. > > Best regards, > Mike mailto:MikePeleah@yahoo.com > From chemistry-request@server.ccl.net Fri Oct 26 15:19:36 2001 Received: from web20703.mail.yahoo.com ([216.136.226.176]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9QJJZB30282 for ; Fri, 26 Oct 2001 15:19:35 -0400 Message-ID: <20011026192229.44811.qmail@web20703.mail.yahoo.com> Received: from [64.3.125.99] by web20703.mail.yahoo.com via HTTP; Fri, 26 Oct 2001 12:22:29 PDT Date: Fri, 26 Oct 2001 12:22:29 -0700 (PDT) From: Masakatsu Watanabe Subject: Re: CCL:free C/C++ compiller for Win32 To: Mike Peleah , chemistry@ccl.net In-Reply-To: <1115040472.20011026190414@yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Mike, Check Cygwin "Unix environment for Windows". It comes with gcc/g++. Cygwin web site is http://sources.redhat.com/cygwin/ I hope it helps you. Masa Watanabe --- Mike Peleah wrote: > Dear chemistry, > > I am looking for a free C/C++ compiller for Win32 > environment. > DJGPP is good but only for DOS. > > Best regards, > Mike > mailto:MikePeleah@yahoo.com > > > > -= 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 > > > > > ===== ========================================================= Masakatsu Watanabe, Ph.D. Wavefunction, Inc. Scientific Developer 18401 Von Karman, Suite 370 E-mail: masa@wavefun.com Irvine, CA 92612, USA Phone: 949-955-2120 FAX: 949-955-2118 Web: http://www.wavefun.com ===========================================================