From chemistry-request@server.ccl.net Wed Jan 3 01:18:19 2001 Received: from gate.sinica.edu.tw (gate.sinica.edu.tw [140.109.4.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA00672 for ; Wed, 3 Jan 2001 01:18:19 -0500 Received: from morgan (MORGAN.nmr.ibms.sinica.edu.tw [140.109.42.134]) by gate.sinica.edu.tw (8.10.1/8.10.1) with ESMTP id f036I4I15464 for ; Wed, 3 Jan 2001 14:18:04 +0800 (CST) Date: Wed, 3 Jan 2001 14:18:06 +0800 From: Jon Wright X-Sender: jon@morgan.nmr.ibms.sinica.edu.tw To: chemistry@ccl.net Subject: Charmm and B-Factors Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone have any pointers/script for calculating B-Factors for specific atoms/residues in a Charmm trajectory? Many thanks Jon From chemistry-request@server.ccl.net Tue Jan 2 13:27:41 2001 Received: from vera.dpo.uab.edu (vera.dpo.uab.edu [138.26.1.112]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA31140 for ; Tue, 2 Jan 2001 13:27:41 -0500 Received: from asc.edu (ZeeMan.tucc.uab.edu) by vera.dpo.uab.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.FDBC9E97@vera.dpo.uab.edu>; Tue, 2 Jan 2001 12:27:26 -0600 Message-ID: <3A521C66.9DD29B2B@asc.edu> Date: Tue, 02 Jan 2001 12:22:30 -0600 From: "Mark A. Zottola" X-Mailer: Mozilla 4.76 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Manual for Hondo8 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking for a manual for Hondo8. There is no documentation contained in the tarball of Hondo8 obtained from QCPE. A dogpile search as well as a search of the CCL archives were equally fruitless. Any help would be greatly appreciated! Best Regards, -- Mark A. Zottola Ph.D. Alabama Research and Education Network 119 Rust Research Center Computer Sciences Corporation 1801 University Boulevard VOICE: (205) 934 - 3893 Birmingham AL 35294 E-MAIL: asnmaz01@asc.edu From chemistry-request@server.ccl.net Wed Jan 3 03:49:16 2001 Received: from earth.ox.ac.uk (root@darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA01261 for ; Wed, 3 Jan 2001 03:49:15 -0500 Received: from dialup-tunnel.earth.ox.ac.uk (darwin [163.1.22.6]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id IAA21459; Wed, 3 Jan 2001 08:49:03 GMT Received: (from keith@localhost) by dialup-tunnel.earth.ox.ac.uk (8.9.3+Sun/8.9.3) id IAA10159; Wed, 3 Jan 2001 08:50:13 GMT From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14930.59328.933813.461933@fermi.nowhere> Date: Wed, 3 Jan 2001 08:50:08 +0000 To: "Hairong Tang" Cc: "CCL" Subject: CCL:Summary: structure of Al2O3 In-Reply-To: <006901c07454$d6818060$de0b140a@lizhenhua> References: <003601c070c9$bd3a0ed0$de0b140a@lizhenhua> <006901c07454$d6818060$de0b140a@lizhenhua> X-Mailer: VM 6.88 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid You omitted to specify which polymorph of Al2O3 you are interested in, alpha, beta or gamma. There are a number of crystallographic databases which you can access in paper or electronic forms from most university libraries. One of the most useful is the "Inorganic Crystal Structure Database", ICSD. http://www.fiz-karlsruhe.de/stn/Databases/icsd.html You may also find something useful on the Amreican Mineralogist database http://www.geo.arizona.edu/xtal-cgi/test Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Wed Jan 3 09:32:16 2001 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03619 for ; Wed, 3 Jan 2001 09:32:15 -0500 Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA19500; Wed, 3 Jan 2001 09:31:03 -0400 Received: from nybc.org (localhost [127.0.0.1]) by iris.nybc.org (SGI-8.9.3/8.9.3) with ESMTP id JAA13592; Wed, 3 Jan 2001 09:33:04 -0500 (EST) Sender: debnath@iris.nybc.org Message-ID: <3A53381F.CF174AB0@nybc.org> Date: Wed, 03 Jan 2001 09:33:04 -0500 From: Asim Kumar Debnath Organization: New York Blood Center X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, adebnath@nybc.org Subject: File conversion - Summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would like to thank to all of you who responded with their suggestions. Following is the summary of responses: ====================================================================== Try dock -i your_file.mol2 -o your_file.pdb See DOCK manual, page 27. Or rerun DOCK, if it is not too long, with mol2 as an output option. Happy New Year. Elizabeth Elizabeth Yuriev ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ You problem can be solved by a small application script. Please download the latest release of the CACTVS toolkit for your platform from our ftp server (ftp://www2.ccc.uni-erlangen.de/pub/cactvs) and install the standard toolkit (unpack in empty, temporary directory, execute the 'installme' script and answer its questions). Next store the following script in a text file (named for example 'convertpdb.tcl'): ------ Dr. Ihlenfeldt was very kind to write this script few times to accomodate my needs and it worked without any problem. Many thanks to him. Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mol2Mol can do this type of conversion, i.e. multiple pdb files to multiple Sybyl mol2 or MDL sdf files. see: www.compuchem.com/mol2mol.htm Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@nybc.org ************** ======================================================================== From chemistry-request@server.ccl.net Wed Jan 3 09:35:43 2001 Received: from web11803.mail.yahoo.com (web11803.mail.yahoo.com [216.136.172.157]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA03670 for ; Wed, 3 Jan 2001 09:35:37 -0500 Message-ID: <20010103143524.17296.qmail@web11803.mail.yahoo.com> Received: from [162.105.177.30] by web11803.mail.yahoo.com; Wed, 03 Jan 2001 22:35:24 CST Date: Wed, 3 Jan 2001 22:35:24 +0800 (CST) From: malin_liu@yahoo.com.cn Subject: disulfide bond in Amber To: chemistry@ccl.net Dear CCLers, How does the Amber force field deal with the disulfide bond formation of CYSs in proteins? What's the standard bond energy (formation)? Any references will be appreciated, thanks a lot. Malin From chemistry-request@server.ccl.net Wed Jan 3 10:50:40 2001 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04085 for ; Wed, 3 Jan 2001 10:50:39 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA27706; Wed, 3 Jan 2001 10:38:22 -0500 (EST) Date: Wed, 3 Jan 2001 10:38:21 -0500 From: Rick Venable To: Jon Wright cc: chemistry@ccl.net Subject: Re: CCL:Charmm and B-Factors In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 3 Jan 2001, Jon Wright wrote: > Does anyone have any pointers/script for calculating B-Factors for > specific atoms/residues in a Charmm trajectory? The COOR DYNA command computes the "average" structure and the isotropic fluctuations about the average for each atom; the latter is is stored in the weigting array (WMAIN). The isotropic fluctuations can be converted to B factor units by multiplying them with the factor (8*pi**2)/3 -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Wed Jan 3 10:29:46 2001 Received: from mtiwmhc25.worldnet.att.net (mtiwmhc25.worldnet.att.net [204.127.131.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03971 for ; Wed, 3 Jan 2001 10:29:46 -0500 Received: from daveg.fsba.com ([12.73.133.118]) by mtiwmhc25.worldnet.att.net (InterMail vM.4.01.03.10 201-229-121-110) with ESMTP id <20010103152731.BFIV29713.mtiwmhc25.worldnet.att.net@daveg.fsba.com>; Wed, 3 Jan 2001 15:27:31 +0000 Message-Id: <5.0.2.1.0.20010103065822.0274ad60@12.17.172.66> X-Sender: davidgallagher@12.17.172.66 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 03 Jan 2001 07:32:45 -0800 To: Sergei Tretiak , chemistry@ccl.net From: David Gallagher Subject: Re: Crystal structure and XYZ coordinates In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Sergei, CAChe includes a crystal builder with all 230 space groups. You select the space group from a pull-down menu and it highlights which parameters are needed. You can paste in or type in the fractional coordinates and then define the size and type of the crystal to be built along each of the three axes. CAChe can also read Shel-X, Cambridge, etc. directly, and handles all elements up to 103. CAChe has won several awards for ease-of-use. The excellent visualization includes coordination polyhedra, thermal ellipsoids and optional full-color stereoscopic. The crystal builder is in all versions of CAChe including Personal CAChe on Windows and Mac at $495 for academics. You can download a free evaluation copy from www.cachesoftware.com or call 503 531 3600 for a CD and any questions. Hope this helps, happy new year, David Gallagher, Fujitsu dgallagher@fujitsu.com Tel: 1 503 746 3607 At 05:53 PM 1/3/01 -0500, you wrote: >Dear Netters: > >Suppose I have cell parameters and would like to >build a piece of crystal and save Cartesian coordinates >of atoms that will be inside of sphere (ellipsoid, cube, >etc.) with given radius. > >What software (free or commercial) could do that? (Easy to >use, options, good visualization capability would be preferences). > >Thanks in advance for a kind consideration of this request. >Have a great 2001! > > Best regards, > > Sergei > > >.-----------------------------------------------------------------------. >|\ / \ | Sergei Tretiak | / \ /| >|.\/...\|.......................................................|/...\/.| >| Theoretical Division | Voice: (505) 667-8351 | >| Mail stop B262 | Fax: (505) 665-4063 | >| Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | >| Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | >| Homepage: http://markov.chem.rochester.edu/serg/welcome.html | >|_______________________________________________________________________| From chemistry-request@server.ccl.net Wed Jan 3 22:34:38 2001 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA06563 for ; Wed, 3 Jan 2001 22:34:37 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id WAA20758 for ; Wed, 3 Jan 2001 22:34:17 -0500 (EST) Date: Wed, 3 Jan 2001 22:34:17 -0500 (EST) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: Basis set for iron in G94 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, I am about running a calculation on an organo-iron compound at both the restricted Hartree-Fock (RHF) as well as the Density Functional Theory (DFT-B3LYP) levels. Two things: =========== (1) I was wondering if you can help me locate or just send me a good basis set for the Fe atom. I will be using a 6-311+G* for the C and H atoms. Appreciate if the format is for GAUSSIAN94. (2) How to select a basis set for Fe out of the many possibilities that exist? Thank you very much, and HAPPY NEW YEAR! Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________