From armel@fluo.univ-lemans.fr Wed Jul 24 07:16:06 1996 Received: from fluo.univ-lemans.fr for armel@fluo.univ-lemans.fr by www.ccl.net (8.7.5/950822.1) id GAA26599; Wed, 24 Jul 1996 06:38:22 -0400 (EDT) Received: from pcb4122.univ-lemans.fr by fluo.univ-lemans.fr (AIX 3.2/UCB 5.64/4.03) id AA16332; Wed, 24 Jul 1996 11:27:09 +0200 Message-Id: <1.5.4.32.19960724103819.00665690@fluo.univ-lemans.fr> X-Sender: armel@fluo.univ-lemans.fr (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 Jul 1996 12:38:19 +0200 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Re: CCL:Crystallographic Software Thanks to Oxford-Cryosystems, however the demo version seems to offer nothing about VRML. If I am not wrong, can we have an URL where to find some .wrl files produced by Crystallographica ? >Crystallographica runs on IBM PC compatible machines running Windows 3.1 = >or 95. Briefly, its main features are: ...... >* Structures may be saved in VRML format, providing stunning graphics = >on any computer with a VRML Viewer. ..... >More information, including a down-loadable demonstration version, is = >available at our Web page (http://www.demon.co.uk/oxcryo/cgraph.html). Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France Tel: (33) 43 83 33 47 Fax: (33) 43 83 35 06 Email: armel@fluo.univ-lemans.fr Home Page: http://fluo.univ-lemans.fr:8001/ From rino@ibc.wustl.edu Wed Jul 24 13:16:13 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id MAA28082; Wed, 24 Jul 1996 12:25:38 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id LAA01378 for ; Wed, 24 Jul 1996 11:26:18 -0500 test-header: [rino@ibc.wustl.edu] Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id LAA17124; Wed, 24 Jul 1996 11:26:45 -0500 Date: Wed, 24 Jul 1996 11:26:45 -0500 (CDT) From: Rino Ragno To: Computational Chemistry List Subject: Zn MM parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers: I am looking for zinc (Zn++) molecular mechanic parameters. Does anybody developed zinc parameters to use in macromodel? All the replies will be summarized. Thank to every one is going to answer. RR ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From rino@ibc.wustl.edu Wed Jul 24 13:16:18 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id MAA28022; Wed, 24 Jul 1996 12:18:52 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id LAA01067 for ; Wed, 24 Jul 1996 11:19:33 -0500 test-header: [rino@ibc.wustl.edu] Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id LAA17075; Wed, 24 Jul 1996 11:19:59 -0500 Date: Wed, 24 Jul 1996 11:19:59 -0500 (CDT) From: Rino Ragno To: chemistry@www.ccl.net Subject: Re: CCL:Conf. space & RBs In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 10 Jul 1996, I wrote the following: > Dear Netters, > > any of you out there knows if there is any program/routine that is able > to compute both the number of rotatable bonds and the number of > geometrically possible number of conformers of a given molecules? > > Thank in advance to every one is going to answer. > > Rino Ragno > Here are the summary of the replies I got: From: Arthur Wang Subject: Re: CCL:Conf. space & RBs I believe that the Systematic Search Module in SYBYL can do this. Arthur ******************** From: brandau@ccgatewy.vchgroup.de Subject: Re: CCL:Conf. space & RBs Dear Rino, have a look at MOLGEN, a structure generator which - if I understand you correctly - should produce just what you want, i.e from a given molecular formula all possible isomers (i.e. connectivities). you can also enter contraints. I can send you brochures if you wish but you might also ask Thomas Wieland at wieland@btm2d1.mat.uni-bayreuth.de, one of the developers, they also have a web page of which I dont't have the address at hand. Sincerely Stefan ******************** From: "Dr. Neil E. Hoare" Dear Rino, Firstly I think most packages e.g. Sybyl, will allow you to do the type of conformational search you require. The program can assign rotatable bonds or you can define the ones you want. I think you have asked a very intresting question about calculating the possible number of conformations. This type of approach requires a criteria for 'when are conformations different ?'. Are you going to consider geometric & torsional rotations only. If so what techniques can you use as a measure of similarity (distance and similarity matrices ?) Example : If we consider a rotation of 30 degrees to be significant enough to cause a change in conformation, for butane (3 rotatable bonds) we have 12^3 = 1728 conformers. I have been studying systems containing 7 rotatable so the above hypothesis leads to 3.6 * 10^7 conformers ! I would like to see a summary of replies if this is available. I hope this is of use, please contact me if you want. Best wishes, Neil -- Neil Hoare PhD CChem MRSC hoaren@sisko.sci.port.ac.uk Tel : (+44) 1705 843623 Centre for Molecular Design Fax : (+44) 1705 843722 University of Portsmouth U.K. ******************** From: Soaring Bear Subject: CCL:Conf. space & RBs The Apex QSAR module from Biosym/MSI has a conformer generator that does this, but you still have to give it parameters of how you want to distinguish conformers by angles, energies, distances. It is pretty easy but expensive. What will your use be? bear _____ ____ bear@ellington.pharm.arizona.edu * ___) * _ \ http://ellington.pharm.arizona.edu/~bear : (___ : |_) : Cyber-Chemist: cancer drug design topo-O O-topo \___ \ | _ < Molecular & Nutritional Biochemist 5'. : : .*** ___) : | |_) : Herbs, Nutrition, Natural Dentistry |'*. .*'| | (_____/oaring |____/ear, UA New Pharmacy 404, Tucson 85721 | | *.,* | | | 3'*,DNA helix| *' Thanks a lot to every one RR ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++