From borghet@ipruniv.cce.unipr.it Fri Jun 6 02:47:08 1997 Received: from ipruniv.cce.unipr.it for borghet@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id BAA14991; Fri, 6 Jun 1997 01:51:45 -0400 (EDT) From: Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA21606; Fri, 6 Jun 1997 07:51:39 +0100 Date: Fri, 6 Jun 1997 07:51:39 +0100 (NFT) Subject: Beta-cyclodextrins-SH To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters I'm interesting in drug transport across the membrane.I would know if someone have functionalized beta-cyclodextrin with an -SH group,and could give me some suggestions . Best wishes Antonello Romani //\\____________________ \\// Antonello Romani Istituto di Patologia Generale Facolta' di Medicina e Chirurgia Univerisita' degli studi di Parma via Gramsci,14 43100 - Parma //\\____________________ \\// From tp@elptrs7.rug.ac.be Fri Jun 6 03:47:09 1997 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.8.3/950822.1) id CAA15197; Fri, 6 Jun 1997 02:47:50 -0400 (EDT) Received: from localhost by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA03128; Fri, 6 Jun 1997 08:47:46 +0200 Date: Fri, 6 Jun 1997 08:47:45 +0200 (DFT) From: "Park, Tae-Yun" To: Ahmed Bouferguene Cc: chemistry@www.ccl.net Subject: Re: CCL:Software to draw curves... In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 5 Jun 1997, Ahmed Bouferguene wrote: > > Hi netters, > > I wonder if somebody knows a site from which one can dowload (for > free) a software drawing curves, functions (given by their explicit > forms), etc... > > Thanks a lot. Try http://www-ocean.tamu.edu/~baum/graphics-graph-systems.html where many different drawing freewares available. Hope this helps. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From walter@came.sbg.ac.at Fri Jun 6 05:47:09 1997 Received: from Agnes.came.sbg.ac.at for walter@came.sbg.ac.at by www.ccl.net (8.8.3/950822.1) id FAA15876; Fri, 6 Jun 1997 05:20:18 -0400 (EDT) Received: from Agnes (localhost [127.0.0.1]) by Agnes.came.sbg.ac.at (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA23277 for ; Fri, 6 Jun 1997 11:19:27 +0200 Sender: walter@came.sbg.ac.at Message-ID: <3397D61F.41C6@came.sbg.ac.at> Date: Fri, 06 Jun 1997 11:19:27 +0200 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: CCL Subject: Potential of Mean Force references Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL readers, I'm looking for references (books, reviews, etc.) about Potential of Mean Force and related things like superposition approximation, pair distribution functions, integral equations, etc. My main interests are applications of these theories to (bio)polymers in solution. Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Email: walter@came.sbg.ac.at =============================================================== From chpajt@bath.ac.uk Fri Jun 6 06:47:10 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA15968; Fri, 6 Jun 1997 06:05:43 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Fri, 6 Jun 1997 11:05:10 +0100 Date: Fri, 6 Jun 1997 11:05:00 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: Abinitio cosmo Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I heard that an implementation of COSMO (or something like it) has been applied to abinitio qm. Does anyone know about this, which code or papers etc? Thanks for any help. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From chan@uni-muenster.de Fri Jun 6 07:47:11 1997 Received: from asterix.uni-muenster.de for chan@uni-muenster.de by www.ccl.net (8.8.3/950822.1) id HAA16181; Fri, 6 Jun 1997 07:22:37 -0400 (EDT) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.7.5/8.7.5) with SMTP id NAA121552 for ; Fri, 6 Jun 1997 13:22:05 +0200 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Fri, 6 Jun 1997 13:22:05 +0200 (MES) From: "Jerry C.C. Chan" To: CCL Subject: 19F chemical shielding tensor calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, One of my colleagues wants to do ab initio and DFT calculations on 19F shielding tensors. Could anyone please give me some references of it (review articles and latest publications). Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** From herrmann@hermes.informatik.uni-stuttgart.de Fri Jun 6 07:59:29 1997 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.8.3/950822.1) id GAA16116; Fri, 6 Jun 1997 06:59:42 -0400 (EDT) Date: Fri, 6 Jun 1997 12:59:39 +0200 Message-Id: <199706061059.MAA00775@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Fri, 6 Jun 1997 12:59:39 +0200 From: Frank Herrmann To: boufer@CeNNAs.nhmfl.gov CC: chemistry@www.ccl.net In-reply-to: (message from Ahmed Bouferguene on Thu, 5 Jun 1997 19:00:16 -0400 (EDT)) Subject: Re: CCL:Software to draw curves... Dear Ahmed, besides the already mentioned programs for curve plotting there is: xgraph for quick display of data files xmgr has more features Regards, --------------------------------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Institute of Parallel and Distributed High-Performance Systems (IPVR) University of Stuttgart Breitwiesenstrasse 20-22 D-70565 Stuttgart (Germany) Tel: (49) 711-7816-358, FAX: (49) 711-7816-250 email: Frank.Herrmann@informatik.uni-stuttgart.de http://www.informatik.uni-stuttgart.de/ipvr/bv/personen/herrmann.html --------------------------------------------------------------------- - Future is alterable but unknown - - Past is known but unalterable - --------------------------------------------------------------------- From ch.etzlstorfer@jk.uni-linz.ac.at Fri Jun 6 10:47:18 1997 Received: from alijku04.edvz.uni-linz.ac.at for ch.etzlstorfer@jk.uni-linz.ac.at by www.ccl.net (8.8.3/950822.1) id JAA17140; Fri, 6 Jun 1997 09:55:38 -0400 (EDT) Received: from [140.78.98.24] (etzlch.chemie.uni-linz.ac.at) by alijku04.edvz.uni-linz.ac.at with SMTP id AA114738 (5.67c/IDA-1.5 for ); Fri, 6 Jun 1997 15:54:50 +0200 X-Sender: k360770@pop.uni-linz.ac.at Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Jun 1997 15:57:09 +0100 To: chemistry@www.ccl.net From: ch.etzlstorfer@jk.uni-linz.ac.at (Christoph Etzlstorfer) Subject: MM3 in TINKER Rencently I downloaded the modeling package TINKER which contains MM3. When calculating the structure of 4,5-dimethylphenantrene I found a torsion angle 4-12-13-5 (the angle on the ringsystem between the methylgroups) of 20.8 degree. In the paper in which MM3 on conjugated hydrocarbons is presented (J. Comp. Chem. 11, p. 868 (1990)) it is 31.9 degree with MM3 and 31.5 degree with X-ray. The structure in the inputfile had a torsion angle of about 35 degree. Does anyone have any experiences with MM3 in TINKER? ################################################################### Dr. Christoph Etzlstorfer Phone: *43-732-2468-750 University of Linz Fax: *43-732-2468-747 A-4040 Linz E-mail: Ch.Etzlstorfer@jk.uni-linz.ac.at Austria http://ocwww.chemie.uni-linz.ac.at ################################################################### From janeou@che.rochester.edu Fri Jun 6 11:47:13 1997 Received: from oz.che.rochester.edu for janeou@che.rochester.edu by www.ccl.net (8.8.3/950822.1) id LAA17637; Fri, 6 Jun 1997 11:04:56 -0400 (EDT) Received: by oz.che.rochester.edu (4.1/1.2che) id AA06539; Fri, 6 Jun 97 11:04:36 EDT Date: Fri, 6 Jun 97 11:04:36 EDT From: Jane-Jane Ou Message-Id: <9706061504.AA06539@oz.che.rochester.edu> To: chemistry@www.ccl.net Subject: Melting Point Prediction Hi, Is there any reference or software which can predict melting point/ freezing point by using computer simulation techniques? Thanks! Jane janeou@che.rochester.edu From lars@lmspc3.ibs.fr Fri Jun 6 12:47:12 1997 Received: from ibs.ibs.fr for lars@lmspc3.ibs.fr by www.ccl.net (8.8.3/950822.1) id MAA18076; Fri, 6 Jun 1997 12:42:29 -0400 (EDT) Received: from lmspc3.ibs.fr (lars@lmspc3.ibs.fr [192.134.36.143]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id SAA22505 for ; Fri, 6 Jun 1997 18:43:36 +0200 Received: (from lars@localhost) by lmspc3.ibs.fr (8.8.5/8.8.5) id SAA26585 for chemistry@www.ccl.net; Fri, 6 Jun 1997 18:39:19 +0200 Date: Fri, 6 Jun 1997 18:39:19 +0200 From: Lars Hemmingsen Message-Id: <199706061639.SAA26585@lmspc3.ibs.fr> To: chemistry@www.ccl.net Subject: CCL: NO3-, CO3--,... polarizabilities Hi all ! I would greatly appreciate all hints for where I may find calculated or experimentally determined polarizabilities for NO3-, CO3--, SO4-- and PO4--- ? yours Lars Hemmingsen From stephen_andruski@fmc.com Fri Jun 6 13:00:31 1997 Received: from igw.fmc.com for stephen_andruski@fmc.com by www.ccl.net (8.8.3/950822.1) id MAA18037; Fri, 6 Jun 1997 12:30:14 -0400 (EDT) Received: by igw.fmc.com id AA19477 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Fri, 6 Jun 1997 11:30:13 -0500 Message-Id: <199706061630.AA19477@igw.fmc.com> Received: by igw.fmc.com (Internal Mail Agent-1); Fri, 6 Jun 1997 11:30:13 -0500 Mime-Version: 1.0 Date: Fri, 6 Jun 1997 12:02:38 -0500 From: stephen_andruski@fmc.com (STEPHEN ANDRUSKI) Subject: Re:MM3 in TINKER To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part I do not have any experience with MM3 in TINKER, but I ran a quick calculation with Alchemy 2000 which also has an implementation of MM3. The angle in question minimized to -31.6 degrees which is in very good agreement with the X-ray structure and the previously published MM3 value. Something in TINKER's implementation must be off. Dr. Stephen W. Andruski FMC Corporation stephen_andruski@fmc.com From howardp@syrres.com Fri Jun 6 15:47:14 1997 Received: from syrres.syrres.com for howardp@syrres.com by www.ccl.net (8.8.3/950822.1) id OAA19019; Fri, 6 Jun 1997 14:54:43 -0400 (EDT) Received: from syrres.com by syrres.syrres.com; Fri, 6 Jun 97 13:37 EST Message-Id: <3.0.32.19970606145529.006f8990@syrres.com> X-Sender: howardp@syrres.com X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 06 Jun 1997 14:55:30 -0400 To: Jane-Jane Ou , chemistry@www.ccl.net From: Phil Howard Subject: Re: CCL:Melting Point Prediction Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 11:04 AM 6/6/97 EDT, Jane-Jane Ou wrote: > > >Hi, > >Is there any reference or software which can predict melting point/ >freezing point by using computer simulation techniques? Thanks! > Jane, We have a program that will predict melting point, boiling point, and vapor pressure from SMILES structural input. See http://esc.syrres.com/~ESC/mpbpvp.htm Phil Philip H. Howard, Ph.D. Phone: 315-426-3350 Environmental Sciences Center Fax: 315-426-3429 Syracuse Research Corporation Email: howardp@syrres.com Merrill Lane http://esc.syrres.com Syracuse, NY 13210 From ponder@dasher.wustl.edu Fri Jun 6 15:56:21 1997 Received: from dasher.wustl.edu for ponder@dasher.wustl.edu by www.ccl.net (8.8.3/950822.1) id PAA19187; Fri, 6 Jun 1997 15:39:50 -0400 (EDT) From: Received: from localhost by dasher.wustl.edu (5.65v3.2/1.1.10.5/12Feb97-1108AM) id AA14433; Fri, 6 Jun 1997 14:39:09 -0500 Message-Id: <9706061939.AA14433@dasher.wustl.edu> Reply-To: ponder@dasher.wustl.edu To: chemistry@www.ccl.net Cc: ponder@dasher.wustl.edu Subject: Comments on the "MM3 in TINKER" thread Date: Fri, 06 Jun 97 14:39:08 -0500 X-Mts: smtp Dear CCL List, In reply to the two messages shown below, we have run calculations on 4,5-dimethylphenanthrene using the TINKER package's version of the MM3 force field. We get a 4-12-13-5 torsion angle of 29 degrees at the "TINKER" minimum. The "official" MM3 value is 32 degrees (31.9) as per Allinger, Li, Yan and Tai, JCC, 7, 868-895 (1990). The crystal structure is 31.5 degrees, MM2 gives 34.6, etc. We need to make the following points: (1) TINKER's MM3 is not exactly the same as "official" MM3. It differs primarily in two respects. TINKER does not implement the "special" functions for the electronegativity, anomeric and Bohlmann corrections. TINKER's conjugated pi-system method for scaling the bond and torsion parameters differs from that used in either MM2 or MM3. It is closer to the MM2 method; PPP-like instead of VESCF, and reparametrized by our group to fit a somewhat different set of conj. hydrocarbons and heterocycles than the JCC paper above. (2) 4,5-Dimethylphenanthrene is a rather extreme case, where the exact value of the angle listed above is quite sensitive to a combination of methyl vdw and pisystem torsional parameters. For example, we used the TINKER MM3 to perform a minimization where the 4-12-13-5 angle is constrained to the X-ray value of 31.5 degrees. The energy of this structure is less than 0.04 kcal/mole higher than the energy of the 29 degree unconstrained TINKER MM3 minimum. For the vast majority of less crowded conjugated systems, we believe that the TINKER MM3 results will be very, very similar to "official" MM3. (3) Given the exceptions listed above in (1), we believe that our MM3 (or for that matter our MM2, AMBER/OPLS, AMBER-95, CHARMM22, and so forth) is essentially EXACT. For a great many molecules, we know our implementation is EXACT by direct comparision with MM3. We have gone to rather great lengths to try to replicate the intentions of the authors of the force fields we have included in TINKER. That said, we should stress that TINKER should not be used as a replacement for "official" MM3, or any other "official" force field. If getting "official" results matters, then we suggest that you use an "official" program.... (4) Christoph Etzlstorfer (1st message below) started this thread by reporting that he got a phenanthrene angle of 21 degrees using TINKER's MM3. We are at a loss to explain his result, and will correspond with him separately. (5) Stephen Andruski (2nd note below) has gotten a value of 31.6 for the dimethylphenanthrene angle using Alchemy 2000. To my knowledge, this should be an "official" MM3 calculation since TRIPOS licences MM3 from Prof. Allinger. The difference between 31.9 in the JCC paper and Andruski's 31.6 might be due to some small change in the "official" MM3 parameters (?). Anyone who would like to try the TINKER molecular mechanics/dynamics package, despite these recent messages to the list, can get the current version 3.3 with full source code from the Ponder lab web site at: http://dasher.wustl.edu/tinker/ A new version 3.4 with many new features, increased speed for some types of calculations and (yes...) some bug fixes will be available from the same site later this month. Jay Ponder ................................................ > The original posting from Christoph Etzlstorfer: > > Rencently I downloaded the modeling package TINKER which contains MM3. When > calculating the structure of 4,5-dimethylphenantrene I found a torsion > angle 4-12-13-5 (the angle on the ringsystem between the methylgroups) of > 20.8 degree. In the paper in which MM3 on conjugated hydrocarbons is > presented (J. Comp. Chem. 11, p. 868 (1990)) it is 31.9 degree with MM3 and > 31.5 degree with X-ray. The structure in the inputfile had a torsion angle > of about 35 degree. > > Does anyone have any experiences with MM3 in TINKER? > > ################################################################### > Dr. Christoph Etzlstorfer Phone: *43-732-2468-750 > University of Linz Fax: *43-732-2468-747 > A-4040 Linz E-mail: Ch.Etzlstorfer@jk.uni-linz.ac.at > Austria http://ocwww.chemie.uni-linz.ac.at > ################################################################### .................................................. > The original posting from Stephen Andruski: > > I do not have any experience with MM3 in TINKER, but I ran a quick > calculation with Alchemy 2000 which also has an implementation of MM3. > The angle in question minimized to -31.6 degrees which is in very > good agreement with the X-ray structure and the previously published > MM3 value. > > Something in TINKER's implementation must be off. > > Dr. Stephen W. Andruski > FMC Corporation > stephen_andruski@fmc.com -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From charwel@chrs1.chem.lsu.edu Fri Jun 6 17:47:15 1997 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id RAA19962; Fri, 6 Jun 1997 17:05:04 -0400 (EDT) Received: by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA41514; Fri, 6 Jun 1997 16:08:24 -0500 Date: Fri, 6 Jun 1997 16:08:24 -0500 (CDT) From: Chris Harwell To: chemistry@www.ccl.net Subject: animation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings netters, we are looking for software (preferably free or cheap) that will 1) draw a molecule (small < 30 atoms) or just balls for atoms are fine 2) animate the picture ie we specify one config in an xyz file then the next frame in another xyz file... 3) AND will alow an additional parameter to be changed like color from frame to frame. (this is to represent the change in charge with time) xmol does great for 1 & 2 and rasmol seems to do fine for 1 and 3 but not 2. we have accessibilty to AIX4.1 on RS6000's, Win95, DOS, and linux redhat 4.2 on pcs, and suns. any suggestions will be greatly appreciated :> thanks, Chris Harwell charwel@chrs1.chem.lsu.edu http://www.chem.lsu.edu/htdocs/people/crharwell/index.html Louisiana State University; 232 Choppin Hall F7; Baton Rouge LA 70803 "Everything positive originates in a positive attitude from someone" :> From JeffAyres@worldnet.att.net Fri Jun 6 21:47:16 1997 Received: from mtigwc03.worldnet.att.net for JeffAyres@worldnet.att.net by www.ccl.net (8.8.3/950822.1) id VAA21364; Fri, 6 Jun 1997 21:31:14 -0400 (EDT) Received: from LOCALNAME ([207.147.169.154]) by mtigwc03.worldnet.att.net (post.office MTA v2.0 0613 ) with SMTP id AAA5743 for ; Sat, 7 Jun 1997 01:30:35 +0000 Message-ID: <3398BA1A.5F5A@worldnet.att.net> Date: Fri, 06 Jun 1997 18:32:10 -0700 From: "Jeffrey J. Ayres" Organization: independent X-Mailer: Mozilla 3.01Gold (Win16; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Babel Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Could anyone help me with a babel conversion problem. The problem is converting 1bna.pdb to 1bna.mol. 1bna is a DNA compound. Another DNA compound also failed to convert, 1d58.pdb. 1crn.pdb, a protein, had no problems converting. The number of atoms in the protein is much greater than the DNA segments. The commands to convert from a pdb file to a molgen file are babel -ip c:\netscape\1bna.pdb -omolgen c:\netscape\1bna.mol The message returned exits the MS-DOS window and says the program was shut down because it violated system integrity. The same message appearred after attempting to convert a DNA structure conversion from .pdb to an ISIS draw file .mol. The conversion input command was -imdl. Has anyone else had a similar problem? If so could you please send me the solution? Thank you, Jeff Ayres