From chemistry-request@server.ccl.net Tue May 11 00:25:56 1999 Received: from punegate.mahindrabt.com (uucp@[203.197.95.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA10509 for ; Tue, 11 May 1999 00:25:46 -0400 Received: (from uucp@localhost) by punegate.mahindrabt.com (8.8.7/8.8.6) id JAA11906 for ; Tue, 11 May 1999 09:56:50 +0530 Received: from intranet.pune.mahindrabt.com(202.41.13.243) via SMTP by punegate.mahindrabt.com, id smtpda11897; Tue May 11 04:26:48 1999 Received: from mahindrabt.com (pc-172-24-7-180.pune.mahindrabt.com [172.24.7.180] (may be forged)) by intranet.pune.mahindrabt.com (8.8.7/8.8.7) with ESMTP id JAA26624; Tue, 11 May 1999 09:49:08 +0530 Message-ID: <3737AE50.F144A37E@mahindrabt.com> Date: Tue, 11 May 1999 09:43:05 +0530 From: "Dr. Sudhir A. Kulkarni" X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@ccl.net, "Dr. Sudhir A. Kulkarni" , "Dr.B.W.Gore" Subject: Summary: FREE MM code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters : Thanks for all those who responded overwhelmingly to my request. It seems TINKER is the most popular MM/MD code which was suggested by : David Reichert Jan Dillen Jens Antony Joe M Leonard Michael Meyer Paul Davis Per-Ola Norrby Smith JA (Jack) Some replies also point to different codes & are given below. I sincerely thank all of them. HI Sudhir Go to the following web site. It has a compilation of most of the software used in computational chemistry. Cheers Amit kulkarni http://www.chem.swin.edu.au/chem_ref.html#Comp __________________________________________________ GROMACS @ http://md.chem.rug.nl/~gmx Groeten, David. _________________________________________________ Don http://www.ks.uiuc.edu/Development/ ______________________________________________ Dear Dr. Kulkarni, Here's another program well worth considering:- AMMP ("Another Molecular Mechanics Program") by Robert Harrison at Thomas Jefferson University. http://asterix.jci.tju.edu/ammp.html -Paul -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk __________________________________________________ Try NAMD at http://www.ks.uiuc.edu/Research/ . NAMD 2.0 source code should be available, so if it is not yet posted on the download page, write to namd@ks.uiuc.edu and ask for it. I hope this helps. Sincerely, Sergei Izrailev sergei@3dp.com _______________________________________________ **************************************************** Sudhir Kulkarni MBT, Pune, India From chemistry-request@server.ccl.net Tue May 11 04:45:45 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12816 for ; Tue, 11 May 1999 04:45:45 -0400 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA22623 Tue, 11 May 1999 04:39:21 -0400 (EDT) Received: from al.bundy.uni-jena.de (al.bundy.uni-jena.de [141.35.147.40]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id KAA09900 for ; Tue, 11 May 1999 10:39:20 +0200 (MET DST) Message-Id: <199905110839.KAA09900@fsuj20.rz.uni-jena.de> Received: by al.bundy.uni-jena.de (1.37.109.4/16.2) id AA25396; Tue, 11 May 99 10:45:20 +0200 From: Michael Braeuer Subject: Large ab initio calculations To: CHEMISTRY@www.ccl.net Date: Tue, 11 May 99 10:45:19 METDST Mailer: Elm [revision: 70.85] Hi, I need to know the approximate size of the largest ab initio calculations done with standard programs so far. Any hint where I could start searching ? Thank you very much in advance Micha -- Michael Braeuer http://www.uni-jena.de/chemie/anders/micha.htm PhD Student E-mail: brauer@al.bundy.uni-jena.de IOMC FSU Jena Tel: ++49/3641/948217 Humboldtstrasse 10 Fax: ++49/3641/948212 07743 Jena Germany From chemistry-request@server.ccl.net Tue May 11 05:39:13 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA13362 for ; Tue, 11 May 1999 05:39:13 -0400 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA22682 Tue, 11 May 1999 05:33:09 -0400 (EDT) Received: from al.bundy.uni-jena.de (al.bundy.uni-jena.de [141.35.147.40]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id LAA15145 for ; Tue, 11 May 1999 11:33:03 +0200 (MET DST) Message-Id: <199905110933.LAA15145@fsuj20.rz.uni-jena.de> Received: by al.bundy.uni-jena.de (1.37.109.4/16.2) id AA27702; Tue, 11 May 99 11:39:09 +0200 From: Michael Braeuer Subject: Slater Determinant To: CHEMISTRY@www.ccl.net (chemistry list) Date: Tue, 11 May 99 11:39:09 METDST Mailer: Elm [revision: 70.85] Hi, does anybody know where the Slater Determinant was first mentioned ? Thank you in advance Micha -- Michael Braeuer http://www.uni-jena.de/chemie/anders/micha.htm PhD Student E-mail: brauer@al.bundy.uni-jena.de IOMC FSU Jena Tel: ++49/3641/948217 Humboldtstrasse 10 Fax: ++49/3641/948212 07743 Jena Germany From chemistry-request@server.ccl.net Tue May 11 07:20:21 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA14289 for ; Tue, 11 May 1999 07:20:21 -0400 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA22832 Tue, 11 May 1999 07:14:16 -0400 (EDT) Received: from localhost by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id NAA18654; Tue, 11 May 1999 13:14:10 +0200 (MET DST) Date: Tue, 11 May 1999 13:14:08 +0200 (MET DST) From: Kris Van Alsenoy X-Sender: alsenoy@inch.uia.ac.be To: Michael Braeuer cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Large ab initio calculations In-Reply-To: <199905110839.KAA09900@fsuj20.rz.uni-jena.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 11 May 1999, Michael Braeuer wrote: > Hi, > > I need to know the approximate size of the largest ab initio > calculations done with standard programs so far. > > Any hint where I could start searching ? you may want to look at a calculation on crambin, a protein containing 46 aminoacids (642 atoms). JPC A, vol. 102, 2246-2251 (1998) by Yu, Peeters, Martin, Sch\"afer and myself. sincerely, kris --------------------------------------------------------------------------- Kris Van Alsenoy, Quantum Chemistry, Structural Chemistry Group, Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Antwerp, Belgium. E-mail : alsenoy@uia.ua.ac.be / Phone : +32(3)8202366 / Fax : +32(3)8202310 --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue May 11 08:44:30 1999 Received: from ck-sg.p.lodz.pl (ck-sg.p.lodz.pl [212.51.207.68]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA15248 for ; Tue, 11 May 1999 08:44:16 -0400 Received: from piotr.p.lodz.pl (pc-212-51-214-182.p.lodz.pl [212.51.214.182]) by ck-sg.p.lodz.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF-1) via SMTP id OAA03535 for ; Tue, 11 May 1999 14:37:13 +0200 (MDT) Message-ID: <007901be9baa$c2c9c020$b6d633d4@p.lodz.pl> From: "Paneth" To: Subject: PM3tm-summary Date: Tue, 11 May 1999 14:35:32 +0200 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 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 I'd like to thank people who responded to my querry regarding PM3tm parametrization. The question was: which implementation of this Hamiltonian gives correct results (Spartan or Hyperchem)? Some people suggested staying away from it, usage of ab initio (MINI), or useage of at least DTF methods. The difference between implementations in the above-mentioned programs was pointed out: in Spartan correction for H-H repulsion is added by default in calculations containing tms. (Unfrotunately I couldn't check if this was my problem since the keyword turning it off does not work in PC Spartan Pro). Finally, thanks to Alan Shusterman, we were able to compare data for CrO3. C3v geometry gave in all versions of Spartan (unix, mac, pc) heat of formation of -79.14 kcal/mol while Hyperchem yielded -185.5 kcal/mol (experimental data: about -52 kcal/mol JPC 1996, 100, 6354) - geometrical results are the same from both programs. Piotr ****************************************************** Professor Piotr Paneth Department of Chemistry, Technical University Zeromskiego 116, 90-924 Lodz, Poland phone/fax: (+48 42) 631-3199 fax: (+48 42) 636-5008 From chemistry-request@server.ccl.net Tue May 11 09:01:59 1999 Received: from ns.DKFZ-Heidelberg.DE (ns.dkfz-heidelberg.de [192.55.188.199]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15447 for ; Tue, 11 May 1999 09:01:54 -0400 Received: from dkfz1.inet.dkfz-heidelberg.de (dkfz1.inet.dkfz-heidelberg.de [193.174.51.93]) by ns.DKFZ-Heidelberg.DE (8.8.8/8.8.8/DKFZ-8.8.8) with ESMTP id OAA25303 for ; Tue, 11 May 1999 14:53:47 +0200 (MET DST) Received: from DKFZ1/SpoolDir by dkfz1.inet.dkfz-heidelberg.de (Mercury 1.31); 11 May 99 14:53:46 GMT+1 Received: from SpoolDir by DKFZ1 (Mercury 1.31); 11 May 99 14:53:36 GMT+1 Received: from DKFZ-heidelberg.de by dkfz1.inet.dkfz-heidelberg.de (Mercury 1.31) with ESMTP; 11 May 99 14:53:32 GMT+1 Sender: tajkhors@ns.DKFZ-Heidelberg.DE Message-ID: <3738A67B.E486FF35@DKFZ-heidelberg.de> Date: Tue, 11 May 1999 14:51:55 -0700 From: Emadeddin Tajkhorshid Organization: German Cancer Research Center X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: ccl CCL Subject: Mg2+ parameters in cvff or cff9x Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I have performed a series of MD simulations using cvff and cff91 force fields of MSI. Now, I would like to add a positively charged Mg atom to my protein and optimize the system. However, I get into trouble with finding the right parameters for the Mg2+. I wonder if the parameters needed for the metal ion are present in the new versions of the force fields or I have to think about adding them manually (right now, I do not know how) to the force field. Thanx in advance -- Emad ********************************************************************* E. Tajkhorshid, Ph.D. German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 http://genome.dkfz-heidelberg.de/users/emad 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Science is talking to each other" * ********************************************************************* From chemistry-request@server.ccl.net Tue May 11 09:26:18 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15720 for ; Tue, 11 May 1999 09:26:17 -0400 Received: from bosoleil.ci.umoncton.ca (bosoleil.ci.umoncton.ca [139.103.2.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA23272 Tue, 11 May 1999 09:20:13 -0400 (EDT) Received: from localhost (sichelj@localhost) by bosoleil.ci.umoncton.ca (8.8.6 (PHNE_15509)/8.8.6) with SMTP id KAA07180; Tue, 11 May 1999 10:16:01 -0300 (ADT) Date: Tue, 11 May 1999 10:16:00 -0300 (ADT) From: "J. Sichel" X-Sender: sichelj@bosoleil.ci.umoncton.ca To: Michael Braeuer cc: chemistry list Subject: Re: CCL:Slater Determinant In-Reply-To: <199905110933.LAA15145@fsuj20.rz.uni-jena.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 11 May 1999, Michael Braeuer wrote: > does anybody know where the Slater Determinant was first mentioned ? J.C.Slater, Phys.Rev. _34_, 1293 (1929) This is the reference given by Slater in his 1960 book Quantum Theory of Atomic Structure (v.1, p.288), and Levine, Quantum Chemistry, 4th edn, p.271 confirms that "Slater pointed out in 1929 that a determinant of the form ... satisfies the antisymmetry requirement for a many-electron atom." John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada E1A 3E9 From chemistry-request@server.ccl.net Tue May 11 10:03:51 1999 Received: from bif1.creighton.edu (bif1.creighton.edu [147.134.148.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA16189 for ; Tue, 11 May 1999 10:03:50 -0400 Received: from bif1.creighton.edu by bif1.creighton.edu (IBM OS/2 SENDMAIL VERSION 2.0/2.12um) id IAA006.94; Tue, 11 May 1999 08:59:02 -0400 Message-ID: <373837A4.18630F8B@bif1.creighton.edu> Date: Tue, 11 May 1999 08:59:01 -0500 From: Sandor Lovas X-Mailer: Mozilla 4.04 [en] (OS/2; U) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Free MM Code Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sudhir Kulkarni posted today the summary of the free MM code available. It really seems that TINKER is the most popular, however, when it comes to MD simulation of peptides or proteins, I think GROMACS package is the best, foer ease of use and it provides a whole bunch of analyses suites. TINKER is very good at energy minimization or MD simulations of structures using different force fields in vacuum or using solvation model, but very weak at MD simulation using solvent box. Best wishes Sandor _________________________________________________________________________________ Sandor Lovas Assistant Professor Phone: 402-280-5753 Department of Biomedical Fax: 402-280-2690 Sciences Creighton University e-mail: vasz@bif1.creighton.edu 2500 California Plaza http://www.creighton.edu/BioMedSci/bms50.htm Omaha, NE 68178 USA _________________________________________________________________________________ From chemistry-request@server.ccl.net Mon May 10 06:14:45 1999 Received: from originqf.uib.es (originqf.uib.es [130.206.133.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32278 for ; Mon, 10 May 1999 06:10:53 -0400 Received: from originqf.uib.es (localhost [127.0.0.1]) by originqf.uib.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id DAA01874 for ; Mon, 10 May 1999 03:11:15 -0700 (PDT) Sender: juan@originqf.uib.es Message-ID: <3736B0C3.167E@originqf.uib.es> Date: Mon, 10 May 1999 03:11:15 -0700 From: Juan Frau Munar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Animations in Power Point Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA32286 Hello everybody I would like to have an active molecule in a Power Point´s slide. We would like to get the molecule rotating 360º during the presentation. It is something similar to the animations we can see on the web (MDL format). Any ideas? Thanks in advance. Juan Frau -- Juan Frau Munar Universitat Illes Balears Departament de Quimica Palma de Mallorca - 07071 Baleares. Spain email: juan@originqf.uib.es fax: 971 - 173426 telf: 971 - 173254 From chemistry-request@server.ccl.net Mon May 10 15:12:17 1999 Received: from ghiberti.pch.nat.tu-bs.de (ghiberti.pch.nat.tu-bs.de [134.169.41.187]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA05741 for ; Mon, 10 May 1999 15:12:16 -0400 Received: from brunelleschi.pch.nat.tu-bs.de by ghiberti.pch.nat.tu-bs.de (5.65v4.0/1.1.19.2/05Mar98-0504) id AA03710; Mon, 10 May 1999 21:06:09 +0200 From: Robert Gdanitz Received: by brunelleschi.pch.nat.tu-bs.de (5.65v4.0/1.1.10.5/02Mar98-0611PM) id AA26259; Mon, 10 May 1999 21:06:09 +0200 Message-Id: <9905101906.AA26259@brunelleschi.pch.nat.tu-bs.de> Subject: clustering of a huge number of conformations To: chemistry@ccl.net (Computational Chemistry List) Date: Mon, 10 May 1999 21:06:09 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit In the special case that N molecular conformations are to be clustered into M sets in order to obtain low-energy structures, one may use an algorithm that needs roughly N x M steps. Provided that M is not too large, the algorithm thus can also be used for large N. The algorithm proceeds as follows: i) look for the conformation which is lowest in energy (N step); ii) compare this conformation with all the others and join similar ones to the cluster (N step); iii) delete the cluster from the original set of yet unclustered conformation (bookkeeping); iv) repeat these steps M times. I have used this algorithm to cluster low-energy molecular crystal structures generated by Monte-Carlo simulated annealing, see: Chem. Phys. Lett. 190 (1992) 391. -- PDr. Robert J. Gdanitz Institut f. Physikalische u. Theoretische Chemie Phone: +49 531 391-5370 Technische Universitaet, Hans-Sommer-Str. 10 Fax: +49 531 391-5396 D-38106 Braunschweig, Germany email: gdanitz@tu-bs.de http://www.tu-bs.de/~gdanitz From chemistry-request@server.ccl.net Tue May 11 20:33:58 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01157 for ; Tue, 11 May 1999 20:33:58 -0400 Received: from mailbox1.ucsd.edu (mailbox1.ucsd.edu [132.239.1.53]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA25948 Tue, 11 May 1999 20:30:50 -0400 (EDT) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.156.10]) by mailbox1.ucsd.edu (8.9.1a/8.9.1) with ESMTP id RAA07221 for <@mailbox.UCSD.EDU:chemistry@www.ccl.net>; Tue, 11 May 1999 17:30:52 -0700 (PDT) Received: from chemcca10.ucsd.edu (chemcca15.ucsd.edu [132.239.156.46]) by chemcca10.ucsd.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id RAA20382 for ; Tue, 11 May 1999 17:30:51 -0700 (PDT) Sender: wriggers@chemcca10.ucsd.edu Message-ID: <3738CBBA.5A0D2014@chemcca10.ucsd.edu> Date: Tue, 11 May 1999 17:30:50 -0700 From: Willy Wriggers Organization: University of California, San Diego, Dept. of Chemistry and Biochemistry X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.6 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: update: multi-res. docking w/ Situs 1.1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Hi all, A new version (1.1) of the free single-molecule, multi-resolution docking package went online at URL http://chemcca10.ucsd.edu/~situs Some of the new features are: - A more powerful and more accurate clustering algorithm to correlate features within structural data sets. - Electron microscopy: support of ASCII, CCP4, SPIDER, and MRC file formats, map file export in CCP4 format for visualization e.g. with Swiss PDB Viewer - Small-angle X-ray scattering: Support for docking of crystal structures to bead models from SAXS refinements (Chacon et al., Biophys. J. 74:2760-2775, 1998) More info can be found online and in the current issue of J. Structural Biology (1999) 125:185-195, URL http://www.academicpress.com/jsb Cheers, Willy -- Willy Wriggers, Ph.D. - Dept. of Chemistry and Biochemistry 0365, University of California, San Diego -- La Jolla, CA 92093. (619)534-2913 (tel), (619)534-7042 (fax). - Dept. of Cell Biology MB25, The Scripps Research Institute -- La Jolla, CA 92037. (619)784-2701 (tel), (619)784-2749 (fax). http://chemcca10.ucsd.edu/~wriggers -- wriggers@ucsd.edu