From SERGEI@ps1515.chemie.uni-marburg.de Wed May 10 06:20:06 1995 Received: from Mailer.Uni-Marburg.DE for SERGEI@ps1515.chemie.uni-marburg.de by www.ccl.net (8.6.10/930601.1506) id GAA09393; Wed, 10 May 1995 06:17:10 -0400 Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA106908; Wed, 10 May 1995 12:16:34 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 10 May 95 12:17:03 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 10 May 95 12:16:34 GMT+2 To: chemistry@ccl.net From: "Sergei Vyboishchikov" Date: 10 May 95 12:16:31 MDT Subject: Gear method Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Message-Id: <21355CD5AEC@ps1515.chemie.uni-marburg.de> Dear Netters: A friend of mine looks for a Fortran source code for solving a system of stiff first-order differential equations implementing the Gear method. Any hints and advices would be appreciated. Thank you in advance Sergei Vyboishchikov Universitaet Marburg E-mail: SERGEI@ps1515.chemie.uni-marburg.de From young@slater.cem.msu.edu Wed May 10 08:35:12 1995 Received: from slater.cem.msu.edu for young@slater.cem.msu.edu by www.ccl.net (8.6.10/930601.1506) id IAA10658; Wed, 10 May 1995 08:30:58 -0400 Received: by slater.cem.msu.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA28989; Wed, 10 May 95 08:32:16 -0400 Date: Wed, 10 May 95 08:32:16 -0400 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9505101232.AA28989@slater.cem.msu.edu> To: chemistry@ccl.net Subject: CBS and properties Hello, I have been reading the complete basis set papers which were referenced on this list last week. It looks like an interesting technique so I'll have to try it. What I am wondering about is the possibility of getting properties such as dipole moments and electrostatic potentials more accurately in a similar manner. My initial response is to say that a simplistic method which defines energy as a linear combination of energies from multiple calculations could easily predict a dipole with the same linear combinations of dipoles. However, a method with many complex integrals in the extrapolation proceedure might present technical difficulties for the extrapolation of properties. I would like to hear comments on the feasibility of extrapolating property values. If there are any references to methods for doing this, please send them to me. Dave Young young@slater.cem.msu.edu -------------------------------------------------------------------------- In conventional ab initio calculations, an initial calculation is done using the central field approximation. Then a second calculation is done to eliminate the errors introduced by that approximation. Often more time is spent correcting for errors in the original calculation than on the original calculation. Why not just avoid making those errors in the first place? -------------------------------------------------------------------------- From oesterei@hrz.tu-freiberg.de Wed May 10 09:20:13 1995 Received: from orion.hrz.tu-freiberg.de for oesterei@hrz.tu-freiberg.de by www.ccl.net (8.6.10/930601.1506) id JAA11373; Wed, 10 May 1995 09:08:23 -0400 Message-Id: <199505101308.JAA11373@www.ccl.net> Received: by orion.hrz.tu-freiberg.de (1.38.193.5/15.6) id AA25555; Wed, 10 May 1995 15:05:57 +0200 From: Ralf Oestereich Subject: NMR calculations with IGLO To: chemistry@ccl.net (Computer Chemistry List) Date: Wed, 10 May 95 15:05:56 MESZ Mailer: Elm [revision: 70.85.2.1] Dear netters! We are looking forward to get in contact with some CCL users who can help us with IGLO, i.e. with the calculation and interpretation of NMR data. Please respond to my Email address at oesterei@orion.tu-freiberg.de Thank you for your attention! -- ---------------------------------------------------------------------------- R. Oestereich oesterei@orion.tu-freiberg.de Insitut fuer Anorganische Chemie Berakademie Freiberg Leipziger Strasse 09596 Freiberg/Sachsen Germany From ars@ari.net Wed May 10 09:50:12 1995 Received: from mtolympus.ari.net for ars@ari.net by www.ccl.net (8.6.10/930601.1506) id JAA13167; Wed, 10 May 1995 09:48:48 -0400 Received: from arsoftware.ari.net (arsoftware.ari.net [198.69.192.82]) by mtolympus.ari.net (8.6.5/8.6.5) with SMTP id JAA16883 for ; Wed, 10 May 1995 09:48:25 -0400 Date: Wed, 10 May 1995 09:48:25 -0400 Message-Id: <199505101348.JAA16883@mtolympus.ari.net> X-Sender: ars@mtolympus.ari.net (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: ars@ari.net (ARSoftware Corporation) Subject: Re:Gear Method Though not fortran, Kinetics for Windows is an easy to use Microsoft Windows based software package for modeling complex chemical reactions and reaction mechanisms. This unique program computes the concentrations of the chemical species in a system as a function of time for multistep reversible reactions, given the reaction mechanism, the forward and reverse rate constants, and the initial concentrations of reactants and products. KINETICS easy to use Windows interface allows you to input complex chemical systems by simply typing in the reaction equations and the associated rate constants. The program automatically formulates the differential equations necessary to describe the kinetics of the chemical system. The rate equations are then numerically integrated using a modified GEAR algorithm. Features: * Systems containing up to 100 reversible reactions can be evaluated. * Each reaction can contain up to 5 reactants and 5 products. Thus, ` mechanisms with individual reactions as high as fifth order can be examined. * Computations on systems containing up to 50 chemical species are possible. * A plotting routine is included for viewing results. For more information, contact ars@ari.net Sincerely, Sat Want S. Khalsa ARSoftware ===================================================== ARSoftware Corporation 8201 Corporate Drive Landover, MD 20785 Phone: (301) 459-3773 FAX: (301) 459-3776 e-mail: ars@ari.net From gregory@wucmd.wustl.edu Wed May 10 09:53:22 1995 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.10/930601.1506) id JAA13178; Wed, 10 May 1995 09:49:29 -0400 Received: from wucmd (wucmd.wustl.edu [128.252.137.1]) by wugate.wustl.edu (8.6.11/8.6.11) with SMTP id IAA09518; Wed, 10 May 1995 08:49:26 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA03703; Wed, 10 May 95 08:30:39 -0500 Date: Wed, 10 May 1995 08:21:40 -0500 (CDT) From: Gregory Nikiforovich Subject: Re: CCL:RMS Fits and Symmetries To: James A Given Cc: chemistry@ccl.net, gilson@indigo14.ccl.net In-Reply-To: <199505051850.OAA18174@tiber.nist.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 5 May 1995, James A Given wrote: > I have what I hope is a common problem. We are generating ligand > conformations for use in drug design. The ligands we use can > contain groups with various symmetries, e.g., benzene rings. > Does anyone know how to take such symmetries into account when > calculating RMS fit? > > As a simple example of the problem that arises, imagine a > molecule with a plane of symmetry through its center. If the > molecule is flipped over and then superposed with the original, > the RMS calculation of the difference between the two should be zero. But a naive > calculation of the RMS will not give zero, because the > pairing of atoms induced by the superposition is not the > identity pairing, i.e., the atom marked '1' in the original > will not be coincident with the atom marked '1' in the copy. The real trick is that in drug design you will have an "important" and "unimportant" atoms (or functional groups). So the only RMS what matters would be related to the "important" groups (i.e.: aromatics, H-bond donors/acceptors, ionized groups, etc.). In reality, you wouldn't encounter situations with the clear symmetry for the "important" groups. (Though, there are exceptions, like the symmetric HIV protease inhibitors.) On the other hand, if you are worried about non-coincidence of your atom "1" to a copy atom "1", what is the difference, if both atoms are the same, as in benzene case ? ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## From gregory@wucmd.wustl.edu Wed May 10 10:05:16 1995 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.10/930601.1506) id KAA13984; Wed, 10 May 1995 10:04:52 -0400 Received: from wucmd (wucmd.wustl.edu [128.252.137.1]) by wugate.wustl.edu (8.6.11/8.6.11) with SMTP id JAA10357; Wed, 10 May 1995 09:04:50 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA03864; Wed, 10 May 95 08:46:02 -0500 Date: Wed, 10 May 1995 08:44:01 -0500 (CDT) From: Gregory Nikiforovich Subject: Re: CCL:RMS FIts and Symmetries To: given@tiber.nist.gov Cc: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 5 May 1995, James A Given wrote: > I have what I hope is a common problem. We are generating ligand > conformations for use in drug design. The ligands we use can > contain groups with various symmetries, e.g., benzene rings. > Does anyone know how to take such symmetries into account when > calculating RMS fit? > > As a simple example of the problem that arises, imagine a > molecule with a plane of symmetry through its center. If the > molecule is flipped over and then superposed with the original, > the RMS calculation of the difference between the two should be zero. But a naive > calculation of the RMS will not give zero, because the > pairing of atoms induced by the superposition is not the > identity pairing, i.e., the atom marked '1' in the original > will not be coincident with the atom marked '1' in the copy. The real trick is that in drug design you will have an "important" and "unimportant" atoms (or functional groups). So the only RMS what matters would be related to the "important" groups (i.e.: aromatics, H-bond donors/acceptors, ionized groups, etc.). In reality, you wouldn't encounter situations with the clear symmetry for the "important" groups. (Though, there are exceptions, like the symmetric HIV protease inhibitors.) On the other hand, if you are worried about non-coincidence of your atom "1" to a copy atom "1", what is the difference, if both atoms are the same, as in benzene case ? ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## From theochem@ctc.com Wed May 10 11:05:13 1995 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.10/930601.1506) id KAA15332; Wed, 10 May 1995 10:59:43 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA19189; Wed, 10 May 1995 10:59:24 -0400 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA24332; Wed, 10 May 95 11:56:10 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9505101556.AA24332@pauling.ctc.com> Subject: thermochemical data (follow-up) To: chemistry@ccl.net (Computational Chemistry List) Date: Wed, 10 May 1995 11:55:33 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 945 Dear All: Yes, the list of chemicals I asked for included energetics (i.e. explosives) and nerve gases. Please be assured (for those of you who asked and for those of you who worry) that this information is needed to study the destruction of such compounds by novel methods, rather than for production or use of those compounds. Concurrent Technologies Corporation is a US Government contractor, and I am working under the Army contract which operates the National Defense Center for Environmental Excellence. Sorry for any worries. Doug -- Douglas A. Smith Principal Technical Staff/Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. I would rather be and optimist and wrong than a pessimist and right. From shenkin@still3.chem.columbia.edu Wed May 10 11:50:12 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id LAA16766; Wed, 10 May 1995 11:39:12 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA28682 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Wed, 10 May 1995 11:39:06 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:gilson@indigo14.ccl.net id AA05515; Wed, 10 May 95 11:39:00 -0400 From: "Peter Shenkin" Message-Id: <9505101138.ZM5513@still3.chem.columbia.edu> Date: Wed, 10 May 1995 11:38:58 -0400 In-Reply-To: Gregory Nikiforovich "CCL:RMS Fits and Symmetries" (May 10, 8:21am) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Gregory Nikiforovich , James A Given Subject: Re: CCL:RMS Fits and Symmetries Cc: chemistry@ccl.net, gilson@indigo14.ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Subject: CCL:RMS Fits and Symmetries On Fri, 5 May 1995, James A Given wrote: > I have what I hope is a common problem. We are generating ligand > conformations for use in drug design. The ligands we use can > contain groups with various symmetries, e.g., benzene rings. > Does anyone know how to take such symmetries into account when > calculating RMS fit? There are several ways of doing this. The way MacroModel/BatchMin does it is to define equivalence pairs of atoms; for example, if you have a phenyl group attached at the 1-position, two equivalence pairs would be defined: 2-6 (the equivalent ortho positions) and 3-5 (meta). When calculating an RMS, our software would do it four times for this ring, trying both possibilities for each pair, and would take the lowest result. Clearly, this could be done more smartly: we could have a mechanism to say that 2 and 3 (ortho and meta on one side of the ring) correspond to 6 and 5 on the other, respectively; then we would have to calculate the best rigid-body superposition and residual RMS only two times, instead of three. A side-chain dressing program I wrote works in torsional space, and does it another way. The program is told that certain dihedral bonds, such as chi2 of a PHE, TYR or ASP, and chi3 of a GLU, have 2-fold symmetry. (Another program might be smart enough to figure this out for itself.) Then any dihedral angle for such a torsion that falls between 180 and 360 degrees gets 180 degrees subtracted from it before it's compared to the analogous torsion in the other system. (Of course, the mechanism is implemented in a general way; n-fold local symmetry can be specified.) Hope this helps, -P. -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From doherty@msc.edu Wed May 10 12:05:13 1995 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.10/930601.1506) id LAA17005; Wed, 10 May 1995 11:50:34 -0400 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA05814; Wed, 10 May 95 10:50:32 -0500 Received: from [137.66.12.173] (mac3.msc.edu [137.66.12.173]) by uh.msc.edu (8.6.8.1/8.6.6) with SMTP id KAA08783; Wed, 10 May 1995 10:50:26 -0500 X-Sender: doherty@uh.msc.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 10 May 1995 10:50:30 -0600 To: "Sergei Vyboishchikov" , chemistry@ccl.net From: doherty@msc.edu (David C. Doherty) Subject: Re: CCL:Gear method At 12:16 PM 5/10/95, Sergei Vyboishchikov wrote: >A friend of mine looks for a Fortran source code for solving a >system of stiff first-order differential equations implementing the >Gear method. Any hints and advices would be appreciated. Although this doesn't have anything to do with the above request, I once saw Richard Gear in the movie "Pretty Woman," and my company sells a "powerful-yet- easy-to-use" program for Windoze which may do something completely different than what you're looking for. But what the heck, here comes the obligatory gratuitous plug anyway: -- On the other hand, you may have some luck poking around at netlib, for instance: http://www.netlib.org/ode/index.html ftp://ftp.netlib.org/ode/index http://www.netlib.org/odepack/index.html ftp://ftp.netlib.org/odepack/index -- A snippet from the odepack description: 1. LSODE (Livermore Solver for Ordinary Differential Equations) is the basic solver of the collection. It solves stiff and nonstiff systems of the form dy/dt = f. In the stiff case, it treats the Jacobian matrix df/dy as either a full or a banded matrix, and as either user-supplied or internally approximated by difference quotients. It uses Adams methods (predictor-corrector) in the nonstiff case, and Backward Differentiation Formula (BDF) methods in the stiff case. The linear systems that arise are solved by direct methods (LU factor/solve). LSODE supersedes the older GEAR and GEARB packages, and reflects a complete redesign of the user interface and internal organization, with some algorithmic improvements. 2. LSODES, written jointly with A. H. Sherman, solves systems dy/dt = f and in the stiff case treats the Jacobian matrix in general sparse form. It determines the sparsity structure on its own (or optionally accepts this information from the user), and uses parts of the Yale Sparse Matrix Package (YSMP) to solve the linear systems that arise. LSODES supersedes, and improves upon, the older GEARS package. --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From gedeck@pctc.chemie.uni-erlangen.de Wed May 10 12:07:28 1995 Received: from faui40.informatik.uni-erlangen.de for gedeck@pctc.chemie.uni-erlangen.de by www.ccl.net (8.6.10/930601.1506) id LAA17041; Wed, 10 May 1995 11:51:26 -0400 Received: from pctc.chemie.uni-erlangen.de (pctc.chemie.uni-erlangen.de [131.188.120.2]) by immd4.informatik.uni-erlangen.de with SMTP id RAA17346 (8.6.12/7.4b-FAU); for ; Wed, 10 May 1995 17:50:52 +0200 Received: from pc1.chemie.uni-erlangen.de by pctc.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA15091; Wed, 10 May 1995 16:50:50 +0100 Received: by pc1.chemie.uni-erlangen.de (AIX 3.2/UCB 5.64/4.03) id AA20214; Wed, 10 May 1995 16:50:47 +0100 Date: Wed, 10 May 1995 16:50:42 +0100 (NFT) From: Peter Gedeck To: chemistry@ccl.net Cc: Peter Gedeck Subject: Announce: MolEdit 1.0.b Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Recently, I announced version 1.0 of my program MolEdit on this forum. Due to the fact that some people had problems to download the files >from my FTP-server I uploaded them to ftp.ccl.net. This is also a newer version of MolEdit (1.0.b) that allows to create HPGL-files of the graphical display, so that the pictures can be used in other programs. Additional information is available at the WWW-page: http://pctc.chemie.uni-erlangen.de/~gedeck/moledit.html To download the program either access my FTP-server (in Europe) at pctc.chemie.uni-erlangen.de (131.188.120.2) in directory /pub/moled or use the CCL archives: via anonymous ftp www.ccl.net in /pub/chemistry/software/MS-DOS/MolEdit via gopher gopher gopher.ccl.net 73 software --> MS-DOS --> MolEdit via WWW: http://www.ccl.net/chemistry.html C.C.Archive --> Software --> software archives --> MS-DOS --> MolEdit via e-mail send a message: select chemistry help overview limit 1MByte size 60kbytes cd software/MS-DOS/MolEdit dir get README get *.exe quit to MAILSERV@ccl.net On both servers you can also find versions of the Babel program. Yours, Peter Peter Gedeck Inst. f. Physikalische Chemie I Egerlandstrasse 3 91058 Erlangen Germany Tel: ++9131 - 85 7335 Fax: ++9131 - 85 8307 E-Mail: gedeck@pctc.chemie.uni-erlangen.de WWW: http://pctc.chemie.uni-erlangen.de/~gedeck/gedeck.html --------------------------------------------------------------------------- MolEdit 1.0.b ************* Editor for Mopac-Files ====================== Introduction ============ MolEdit is an editor specially designed to prepare input-files for quantum-chemical programs. During the construction of an input-file it is always possible to check the correctness of the defined structure. In case of errors MolEdit provides informative error messages for the implemented input formats. In addition the combination of the editor with a molecule-viewer allows to examine the defined geometrical structure. This is especially valuable for the creation of z-matrices. The molecule-viewer allows to rotate and to translate the molecule. The structure can be displayed in five different ways: o Wire-frame o Ball-and-Stick o Dot-clouds o Grid o Spheres The combination of an editor with a molecule-viewer will make it very easy for beginning students to learn to write z-matrices. Other features included in MolEdit are: o Formatting input-files o Converting between different formats (Mopac <=> GIP) o Deleting Dummy-Atoms o Inserting and deleting of atoms (while keeping the references correct). o Creation of HPGL-files In the current version MolEdit fully supports several file formats. These are: o The Mopac file format, which is used by the semiempirical program packages Ampac, Mopac and Vamp. o The GIP (geometry-interchange-program) format o The Xmol format Other file formats, among those the Gaussian-file formats are accessible through the conversion utility Babel. MolEdit provides a interface that simplifies the usage of Babel. MolEdit is also able to load, edit and save UNIX-Files. The is useful, if UNIX-filesystems are mounted via NFS. MolEdit is a DOS-application written for the IBM-PC-AT and needs a VGA or EGA-card, either monochrome or color. A coprocessor is recommended but not necessary. In case the real-mode-version of the program is used, either the use of expanded-memory or of a disk-cache is recommended. The program was tested with monochrome-VGA-cards and should adjust itself to this mode. From robert@bert.chem.wsu.edu Wed May 10 13:05:13 1995 Received: from cheetah.it.wsu.edu for robert@bert.chem.wsu.edu by www.ccl.net (8.6.10/930601.1506) id NAA18709; Wed, 10 May 1995 13:04:24 -0400 Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.6.10/WSUit-1.1) with SMTP id KAA25684 for ; Wed, 10 May 1995 10:04:22 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA06332; Wed, 10 May 1995 10:04:30 -0700 From: robert@bert.chem.wsu.edu (Robert B. Yelle) Message-Id: <9505101704.AA06332@bert.chem.wsu.edu> Subject: PDQP To: CHEMISTRY@ccl.net Date: Wed, 10 May 1995 10:04:30 -0800 (PDT) X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 798 Hello, I am currently attempting to calculate electrostatic potential derived charges for asymmetric biomolecules using the program GAMESS. In the publication 'Derivation of Net Atomic Charges from Molecular Electrostatic Potentials' (J. Comp. Chem. 11(3):293-310) the authors, Woods, et al. describe a program called PDQP which symmetrically distributes the atomic points about a cartesian axis so that the ESP calculations work properly in GAMESS. I am seeking information about this program so that I may use it. Does anyone know about this program or know where I may obtain it? Thank you in advance for any and all responses. Rob -- Robert B. Yelle Dept. of Biochemistry/Biophysics Washington State University Pullman , WA 99164-4660 (509) 335-4083 EMAIL: robert@bert.chem.wsu.edu From glee@chem0sun.calstatela.edu Wed May 10 23:35:24 1995 Received: from neptune.calstatela.edu for glee@chem0sun.calstatela.edu by www.ccl.net (8.6.10/930601.1506) id XAA29669; Wed, 10 May 1995 23:31:29 -0400 Received: from chem0sun.calstatela.edu (chem0sun.calstatela.edu [130.182.171.14]) by neptune.calstatela.edu (8.6.9/8.6.9) with SMTP id UAA17076 for ; Wed, 10 May 1995 20:29:47 -0700 Received: by chem0sun.calstatela.edu (4.1/SMI-4.1) id AA14047; Wed, 10 May 95 20:27:02 PDT Date: Wed, 10 May 95 20:27:02 PDT From: glee@chem0sun.calstatela.edu (Ging Lee 12-06-90) Message-Id: <9505110327.AA14047@chem0sun.calstatela.edu> To: chemistry@ccl.net Subject: Spartan 3.0 command Dear netters, Can someone please tell me how to go about simulating a thermodynamic annealling process using command available from Spartan 3.0 package. The system I want to minimize is a twelve units polystyrene oligomer. I have been using MM3 force field available from the package, but I want to take it one step further. Thanks a lot. Ging Lee glee@chem0sun.calstatela.ede glee@chem0sun.calstatela.edu From graham@sentex.net Wed May 10 23:50:22 1995 Received: from granite.sentex.net for graham@sentex.net by www.ccl.net (8.6.10/930601.1506) id XAA29867; Wed, 10 May 1995 23:43:34 -0400 Received: from gu-ttyd6.sentex.net (gu-ttyd6.sentex.net [204.50.3.55]) by granite.sentex.net (8.6.5/8.6.9) with SMTP id XAA00129; Wed, 10 May 1995 23:55:48 -0400 Message-Id: <199505110355.XAA00129@granite.sentex.net> X-Sender: graham@mail.sentex.net X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 10 May 1995 23:43:24 -0400 To: given@tiber.nist.gov (James A Given), chemistry@ccl.net From: graham@sentex.net (Graham Hurst) Subject: Re: CCL:RMS Fits and Symmetries Cc: gilson@indigo14.ccl.net At 02:50 PM 5/5/95 -0400, James A Given wrote: > I have what I hope is a common problem. We are generating ligand >conformations for use in drug design. The ligands we use can >contain groups with various symmetries, e.g., benzene rings. >Does anyone know how to take such symmetries into account when >calculating RMS fit? [Snip] > Is there provision in standard software packages for handling this >problem? The conformational search program that I wrote which is part of the ChemPlus set of extensions for HyperChem optionally handles this problem, without the need to specify equivalent pairs. If the option is turned on, the program initially permutes atom indices to find topologically equivalent atom orders. Although in the worst case this would require comparing N! permutations, in practice the program avoids generating permutations where the elements or coordination don't match that of the initial atom order. The permutations that it does generate are topologically compared to the orginal and those that match are retained for use in RMS comparisons. The program can also neglect hydrogens or only consider specified atoms to further reduce the dimensionality. Thus for cyclohexane with hydrogens ingored, it would use 12 permutations of the atom order for RMS comparisons. I'm not sure if the program suits your purposes, since it doesn't actually report the RMS differences. Rather it uses RMS deviations (after faster initial screening comparisons) to determine whether a produced conformation is equivalent to any already found. The "match" thresholds and tests are user adjustable. At 11:38 AM 5/10/95 -0400, Peter Shenkin wrote: >There are several ways of doing this. The way MacroModel/BatchMin >does it is to define equivalence pairs of atoms; for example, >if you have a phenyl group attached at the 1-position, two equivalence >pairs would be defined: 2-6 (the equivalent ortho positions) and 3-5 >(meta). When calculating an RMS, our software would do it four times >for this ring, trying both possibilities for each pair, and would take >the lowest result. > >Clearly, this could be done more smartly: we could have a mechanism >to say that 2 and 3 (ortho and meta on one side of the ring) correspond >to 6 and 5 on the other, respectively; then we would have to >calculate the best rigid-body superposition and residual RMS only >two times, instead of three. For ChemPlus/HyperChem, one doesn't need to specify the equivalent atom pairs. One checks the "Use equivalent atom orders" option in a dialog box, and for this case it would only do up to two RMS comparisons. (If the first was within a specified threshold it wouldn't bother with the second.) I'm curious to know if any other programs can systematically determine and use equivalent atom orders for RMS comparisons... Cheers, Graham ------- Graham Hurst, PhD or Cambridge, Ontario, Canada