From microsim@nis.net Tue Sep 17 01:12:12 1996 Received: from maple.nis.net for microsim@nis.net by www.ccl.net (8.7.5/950822.1) id AAA12387; Tue, 17 Sep 1996 00:15:00 -0400 (EDT) Received: from FORCE by maple.nis.net with smtp (Smail3.1.28.1 #2) id m0v2rV6-00106QC; Tue, 17 Sep 96 00:11 EDT Message-ID: <323E508E.21A@nis.net> Date: Tue, 17 Sep 1996 00:17:34 -0700 From: Willie Cui Organization: MicroSimulations X-Mailer: Mozilla 2.02E-KIT (Win95; U; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: AccuModel, An Intuitive Program for Creating Accurate 3D Models Using the MM3 Force Field X-URL: http://www.ccl.net/ccl/welcome.html#4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit MICROSIMULATIONS CORP. ANNOUNCES THE RELEASE OF ACCUMODEL, THE FIRST PRODUCT OF THE CHEMINFO-3D FAMILY OF SOFTWARE TO CREATE, ANALYZE AND EVALUATE 3D CHEMICAL STRUCTURES ON DESKTOP COMPUTERS MAHWAH, New Jersey-August 28, 1996-MicroSimulations Corp., an exciting new innovator of molecular design, visualization, and analysis software, today announced it's ChemInfo 3D family of applications to build, visualize, and analyze molecular structures and associated functionality that will enable chemists to accelerate the discovery process. The first product from this series, AccuModel, are released today. Another product, PowerFit, will be introduced in another posting. A number of products are in beta test and will be released this fall, including Property3D for calculating molecular properties based on 3D structures, BioPad for protein sequence drawing and display, and PowerDock for molecular docking. The features in AccuModel 1.0 give chemists the capability to build, view and analyze chemical structures on their PC or PowerPC desktop. The chemist can build a structure using the fragment library, or can import 2D drawings from ISIS/Draw or ISIS/Base. The drawing can be converted automatically into 3D, and can be viewed in wire-frame, ball-stick, and CPK models. Analysis features include distance, bond angle, and torsion measurements. Moreover, the chemist can activate the MM3 force field to enable quick and accurate structural optimization. MM3 was developed by Prof. Norman Allinger, University of Georgia, and is widely accepted as the most accurate molecular mechanics force field. Designed for pharmaceutical and biotechnology companies, ChemInfo3D desktop system enables medicinal chemists to visualize, analyze and evaluate chemical structures and is essential to efficient, productive molecular research. AccuModel is for use on Windows 95, Windows NT, and PowerPC and are available for immediate delivery. For more information, please visit MicroSimulations' Web site, http://www.microsimulations.com -- Willie Cui, Ph.D. Director of Product Development MicroSimulations voice: (201)512-0486 fax: (201)512-0489 http://www.microsimulations.com From microsim@nis.net Tue Sep 17 01:36:59 1996 Received: from maple.nis.net for microsim@nis.net by www.ccl.net (8.7.5/950822.1) id AAA12430; Tue, 17 Sep 1996 00:31:19 -0400 (EDT) Received: from FORCE by maple.nis.net with smtp (Smail3.1.28.1 #2) id m0v2rkt-00106QC; Tue, 17 Sep 96 00:27 EDT Message-ID: <323E5434.5DF5@nis.net> Date: Tue, 17 Sep 1996 00:33:08 -0700 From: Willie Cui Organization: MicroSimulations X-Mailer: Mozilla 2.02E-KIT (Win95; U; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: PowerFit, An Powerful Program for Molecular Fitting Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit MICROSIMULATIONS ANNOUNCES RELEASE OF POWERFIT, AN POWERFUL PROGRAM FOR MOLECULAR FITTING. MAHWAH, New Jersey-August 28, 1996-MicroSimulations Corp., an exciting new innovator of molecular design, visualization, and analysis software, today announced the release of PowerFit, the second product from it's ChemInfo 3D family of applications. The first product from this series, AccuModel, is designed for the construction of accurate 3D molecular models using the MM3 Force Field and is introduced in a seperate posting. Complementary to AccuModel, PowerFit enables the chemists to "fit", or compare, one structure to another. Manual or automated, rigid-body or conformational flexible fitting. The fitting potential is based on the work of Kearsley and Smith and known as "Steric and Electrostatic ALignment (SEAL). The global search of the best fit is enabled using Monte Carlo simulated annealing The user interface is very visual and intuitive. Molecules can be controlled manually for detailed visual comparison. User can actually observe the dynamic "fitting" process. Designed for pharmaceutical and biotechnology companies, ChemInfo 3D desktop system enables medicinal chemists to visualize, analyze and evaluate chemical structures and is essential to efficient, productive molecular research. PowerFit is for use on Windows 95, Windows NT, and PowerPC and is available for immediate delivery. For more information, please visit MicroSimulations' Web site, http://www.microsimulations.com About MicroSimulations Established in 1993, MicroSimulations Corp. offers an exciting suite of integrated molecular design, visualization, and analysis software used in pharmaceutical, chemical, agrochemical, and biotechnology research and development. MicroSimulations' innovative products enable individuals, research teams, and organizations to leverage intellectual assets by allowing scientist to enhance their intuition through the use of powerful yet highly cost-effective applications designed to speed new product discovery. -- Willie Cui, Ph.D. Director of Product Development MicroSimulations 478 Green Mountain Road Mahwah, NJ 07430 voice: (201)512-0486 fax: (201)512-0489 http://www.microsimulations.com From owner-chemistry@ccl.net Tue Sep 17 05:12:14 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id EAA13621; Tue, 17 Sep 1996 04:38:17 -0400 (EDT) Received: from beba.cesnet.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.5/950822.1) id EAA17430; Tue, 17 Sep 1996 04:38:13 -0400 (EDT) Received: from ns.karlov.mff.cuni.cz (ns.karlov.mff.cuni.cz [193.84.60.3]) by beba.cesnet.cz with SMTP id KAA13108 (8.6.12/IDA-1.6 for ); Tue, 17 Sep 1996 10:38:09 +0200 Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa00875; 17 Sep 96 10:37 MESZ Received: from silicon by silicon.karlov.mff.cuni.cz via SMTP (940816.SGI.8.6.9/930416.SGI) for id HAA05881; Tue, 17 Sep 1996 07:56:58 -0700 Sender: strajbl@silicon.karlov.mff.cuni.cz Message-ID: <323EBC39.41C6@silicon.karlov.mff.cuni.cz> Date: Tue, 17 Sep 1996 07:56:57 -0700 From: Marek Strajbl X-Mailer: Mozilla 3.0b8Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computer Chemistry List Subject: optimization to TS of THF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I am trying to find transition strucutre of tetrahydrofuran (THF) at HF/6-31G*, BLYP/6-31G* and B3LYP/6-31G* levels. I started computations from O-exo geometry, that is expected for TS, but computations do not converge. I tried optimization in internal, redundant, cartesian coordinates, QST3 method.I switched off testing of the number of eigenvalues, as the program (gaussian 94) complained about wrong number of negative eigenvalues. But nothing works. Can sombody give me a hint how to overcome these problems. Thanks, Marek -- Marek Strajbl Institute of Physics, Charles University e-mail: From Geoffrey@averell.umh.ac.be Tue Sep 17 05:38:03 1996 Received: from averell.umh.ac.be for Geoffrey@averell.umh.ac.be by www.ccl.net (8.7.5/950822.1) id EAA13722; Tue, 17 Sep 1996 04:53:10 -0400 (EDT) From: Received: by averell.umh.ac.be (AIX 3.2/UCB 5.64/4.03) id AA24688; Tue, 17 Sep 1996 10:50:21 +0200 Message-Id: <9609170850.AA24688@averell.umh.ac.be> Subject: Pseudo. in G94_summary To: chemistry@www.ccl.net (CCL Computational Chemistry List) Date: Tue, 17 Sep 1996 10:50:21 +0100 (DFT) X-Mailer: ELM [version 2.4 PL0] Content-Type: text Dear CCL, Here is the summary of the answers that i received for my request of informations about pseudopotentials paramaters and basis for heavy metals in Gaussian94. I would like to present my apologizes because i can't mention all the people who have answered me due to computers'troubles. So, even if i can't mention everybody, i would like to thank you. Best regards, Geoffrey Pourtois Hi, You will find the lanl2dz ecp's within G94. Nevertheless, you can find more ecp's in the site "http://odyssey.pnl.gov:2080/forms/basisform.html". Hope this helps. Regards, Reinaldo Pis_Diez Bonjour Geoffrey, Vous pouvez regarder la page web suivante ou vous trouverez des pseudopotentiels pour l'ensemble (pratiquement !!) du tableau periodique. Ceux-ci ont ete developpes a Stuttgart et font partie des pseudos les plus utilises a l'heure actuelle. http://www.theochem.uni-stuttgart.de/ Vous pouvez recuperer directement les fichiers de pseudopotentiels a partir du tableau periodique. N'oubliez pas de recuperer le fichier Readme qui donne des explications sur le format des fichiers. Si vous avez des questions sur la facon de les implementer dans Gaussian94 (la notice etant bourree d'erreurs a ce niveau !!), n'hesitez pas a me contacter. Cordialement, Laurent Joubert **************************************************************** * Geoffrey Pourtois, PhD student * * Service de Chimie des Materiaux Nouveaux * * Center for Research in Molecular Electronics and Photonics * * University of Mons-Hainaut * * 20, Place du Parc, B-7000 Mons, BELGIUM * * e-mail : Geoffrey@averell.umh.ac.be * * fax : +32 65 37 3366 * * +32 65 37 3054 * * tel : +32 65 37 3363 * **************************************************************** From Jeffrey.Gosper@brunel.ac.uk Tue Sep 17 05:55:35 1996 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id EAA13665; Tue, 17 Sep 1996 04:46:40 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Tue, 17 Sep 1996 09:46:30 +0100 Date: Tue, 17 Sep 1996 09:46:29 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:fractional coordinates > full data To: chemistry@www.ccl.net cc: Jeffrey.Gosper@brunel.ac.uk Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear computational chemistry and other interested parties, Here are the replies I received concerning my recent query about fractional coordiantes to full XYZ data. Original posting: Dear all, I was wondering what non-commerical software is around that will take primative fractional unit cell coordinates and space group information and generate orthogonal atomic coordinates for all atoms in a unit cell. Cheers Replies with comments. ********************* Jeffrey, Despite the fact that you develop a code which is NOT available for the Mac, I will still give some free advice!!! Julian Gale's program GULP which is a very powerful code for simulating crystals can take the fractional coordinates and space group of a crystal and generate a full set of cartesian coordinates. Julian's email address is: gale@ri.ac.uk Andrew Rohl Comment/reply from JJG: Thanks Andrew for the information about GULP. I will have to get hold of a copy. Also most sincerely applogies for my PC bias. The fact is I program in Visual Basic (in order to readily produce Windows programs) and to the best of my knowledge there is no equivalent on the MAC. Can't the MAC emulate (or run) Windows3/95/NT? *********************** there is always the old standby - ortep (OakRidge Thermal Ellipsoid Program) now available in an executable form that runs straight away on most PC's. The full printed output option will provide this. It can be downloaded for free from their web site http://www.ornl.gov/ortep/ortep.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu ************************* Check out the combinations of programs called matfract.c fract2xyz.c available at (you can also get to them from the link on my list of publications of my home page, see below): gopher://www.ccl.net:73/00/software/SOURCES/C/fractional_coordinates /matfract.c gopher://www.ccl.net:73/00/software/SOURCES/C/fractional_coordinate s/fract2xyz.c It will not take the spacegroup information, but allows you to generate the rest of the molecules using matrix operations in fraction coordinate space (matfract), and convert the output of that into cartesian coordinates using fract2xyz. Rene P.F. Kanters, Ph. D. Chemistry Project Specialist Chemistry Department University of Richmond, VA 23173 phone: (804) 287-6873 www: http://www.science.urich.edu/~kanters/ *************************** Dear Dr. Gosper, recently I had the same problem as you and wrote a corresponding FORTRAN program, using some existing subroutines I had already. You can have the code if you like (on your own risk, of course). I found the program to work well. It constructs the unit cell from fractional coordinates and the space group information. The latter must be given in a simplified format. To perform \hat y, \hat x, z + 1/2 you must input three lines: 2 1 3 (permutation) -1. -1. 0. (reflection) 0. 0. 0.5 (translation) This must be done for every symmetry operation. In addition you tell the program to construct more than one unit cell, e.g. to construct a MD simulation box. If this is what you need, send me a mail. Best wishes, Gerald Kneller -- Dr. Gerald Kneller Science Division, Group TOFHR Institut Laue-Langevin B.P. 156 F-38042 GRENOBLE CEDEX 9 Tel.: (33) 76207516 Fax.: (33) 76483906 Comment/reply by JJG: Sounds interesting and very similar to what I had in mind so please forward a copy. I hope to get a student working on a Windows version of this very soon. I think we'll add a database of symmtery operations which will be automatically picked up when the space group is entered. ************************ Dear Jeffrey, I have recently wondered the same. A summary of any replies, either via the list or directly to me would be much appreciated. Regards, Cedric. ************************ Dear Dr. Gosper, INTERCHEM does what you want (and much more). It is not strictly speaking non-commercial, but to academic institutions it sells for £400 (or free if you are prepared to plead extreme poverty!). The dowmside is that it works only on SGI platforms. For information see the web-site:- http://interchem.chem.strath.ac.uk/inter/interprobe.html Yours sincerely, Peter Bladon ************************ Hello. Check out the crystallography archive on the web, and see about XPMA/Zortep from Laslo Zolnai, or possibly STRUPLO, (which has evolved? into STRUVIR). There are some other programs or subroutines possibly of interest there, but those two are the ones I've used in the past. If you find something not on the list that looks useful, please let me know, as coordinate (and kpoint) generation is always an issue in our group. (Professor Burdett, Solid-state theory). -fred Frederick P. Arnold, Jr. The University of Chicago: Dept. of Chem., U. of Chicago Where the End of the World Began. 5735 S. Ellis Ave Chicago, IL 60637 ********************** don't know about non-commercial. I use Alchemy III from Tripos Assoc. which is not an expensive programme, to do just this - in fact, it's about the only useful thing Alchemy does, but that's another story... (address withheld by Jeff Gosper as I don't want to start a flame war. ********************** Jeffrey, I enclose 'tid-bits' of what I think you need to carry out your task. The program is written in Fortran and is 'as is'. Carlos PROGRAM CRYSTSYM C generates crystallographic symmetry coordinates naturally from frac.coords. C ###rest of program cut### carlos@penelope.bio.cornell.edu (Carlos Faerman) comment by JJG: Interesting I'll spend so time looking at this, thanks. ********************** Quanta will for Cambridge FDAT files. And many programs can handle PDB files, which are orthogonal Angstrom coords, but need conversion back to fractional in order to allow symmetry operations. Regards, Leif Norskov Novo Nordisk A/S Copenhagen Denmark lnl@novo.dk comment by JGG: Is Quanta free? I don't think so. **************************** Dear Jeffrey, Check out the freeware program called Babel, available at http://mercury.aichem.arizona.edu/babel.html It is available for a variety of platforms, and will convert coordinate data from almost any standard or proprietary format to almost any other. Yours, Dale Braden Dept. of Chemistry Univ. of Oregon genghis@darkwing.uoregon.edu comment by JJG: I don't think BABEL can really do this. It may be able to translate the primative positions to XYZ but not produce the full cell (or multipl cells). /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From mbskowro@cyf-kr.edu.pl Tue Sep 17 06:12:13 1996 Received: from info.cyf-kr.edu.pl for mbskowro@cyf-kr.edu.pl by www.ccl.net (8.7.5/950822.1) id GAA13988; Tue, 17 Sep 1996 06:11:15 -0400 (EDT) Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.4.10]) by info.cyf-kr.edu.pl (8.7.5/8.7.5) with ESMTP id MAA20395 for ; Tue, 17 Sep 1996 12:10:46 +0200 (METDST) Received: (from mbskowro@localhost) by kinga.cyf-kr.edu.pl (8.7.5/8.7.3) id MAA05135 for chemistry@www.ccl.net; Tue, 17 Sep 1996 12:10:43 +0200 (METDST) From: Marek Skowronek Message-Id: <199609171010.MAA05135@kinga.cyf-kr.edu.pl> Subject: summary: MD of ions in NaCl solution To: chemistry@www.ccl.net Date: Tue, 17 Sep 1996 12:10:43 +0200 (METDST) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear Netters, I am sending the summary about a molecular dynamics in NaCl solution. I would like to thank Thomas Huber and Pascal Auffinger for their answers that are very helpful for me. Here is my problem that sent some weeks ago. I have been simulating a behaviour of several molecules in water using Amber program. However, some interesting phenomena take place in 0.9% NaCl solution. These molecules, that are ions, have two SO3- groups which play an important role in their interactions. I would like to take into consideration an influence of Na+ ions in my simulations. In the Amber's manual they suggest using CION program. I am not sure what might be the best way to do this. I should be very grateful for any further comments, advice, references. I will send the second summary as soon as possible. Thank you in advance. Marek Skowronek Here are the answers: ========================================================================= From Thomas Huber Marek, Do you want to perform an explicit water simulation, I guess yes. Then 0.9% NaCL = 150 mM, i.e. 1 Na+, 1Cl+ per 367 H2O. At what concentration do you want to simulate the molecules (you said they are ions) ? I would say, you have to simulate a very large system, e.g. 3700 Water, to have only some statistically meaningful answers. Try to use a higher concentration of NaCl. Then 2nd, you will have to include long range electrostatics. With Amber 4.1 the particle mesh ewald summation (PME) method would be ok. Another method, neglecting longe range electrostatics, is to include polarization of water and non-additive three body nonbonded interactions. A paper from Peter Kollman showed the advantage of this potential. It was some 1992 (or 91) in JACS. (Dang&Kollman ??) Thomas ========================================================================== From Pascal Auffinger Hi Marek, Please take a look at : P. Auffinger, D.L. Beveridge, Chem. Phys. lett. 234 - 1995 - 413-415 Pascal =========================================================================== From leclerf@MEDCN.UMontreal.CA Tue Sep 17 10:13:15 1996 Received: from condor.CC.UMontreal.CA for leclerf@MEDCN.UMontreal.CA by www.ccl.net (8.7.5/950822.1) id JAA14783; Tue, 17 Sep 1996 09:19:06 -0400 (EDT) Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by condor.CC.UMontreal.CA with ESMTP id NAA11079 (8.6.11/IDA-1.6 for ); Tue, 17 Sep 1996 13:16:54 GMT Received: from med07.MEDCN.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id JAA10160; Tue, 17 Sep 1996 09:19:29 -0400 Received: by med07.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id JAA05147; Tue, 17 Sep 1996 09:19:28 -0400 Date: Tue, 17 Sep 1996 09:19:28 -0400 From: leclerf@MEDCN.UMontreal.CA (Leclerc Fabrice) Message-Id: <9609170919.ZM5145@med07.MEDCN.UMontreal.CA> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: CCL: summary homology modeling Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, Here is the summary concerning the validation of homology or comparative modeling methods; the original posting was: I'm looking for examples of homology modeling methods validated by the comparison between the model built and the known structure determined by = X-ray crystallography. Any reference about such examples ? ******************************Summary*************************************** On Sep 12, 8:48am, Stefan Grzybek wrote: > Subject: Re: CCL:homology modeling > On Sep 11, 6:44pm, Leclerc Fabrice wrote: > > Subject: CCL:homology modeling > > > > Dear Fabrice, > > There has been a sort of 'contest' to this subject, whose results are published > in the whole issue of Proteins Vol. 23, 1995. One of the refernces therein is > the following: > > @article{ 405, > AUTHOR = {{\v{S}}ali, A. and Potterton, L. and Yuan, F. and van > Vlijmen, > H. and Karplus, M.}, > TITLE = {Evaluation of Comparative Protein Modeling by {\sc Modeller}}, > JOURNAL = {Proteins}, > YEAR = {1995}, > VOLUME = {23}, > PAGES = {318--326}, > } > > Hope this helps, > Stefan > > -- > | Stefan Grzybek email: grzybek@athena.chemie.uni-erlangen.de | > | http://athena.chemie.uni-erlangen.de/~grzybek | > | Universitaet Erlangen, Institut fuer Physikalische und Theo- | > | retische Chemie, Egerlandstr. 3, D-91058 Erlangen, Germany | > | Voice: +49 +9131 857318, Fax: +49 +9131 858307 | On Sep 12, 8:53am, Jeffrey L. Nauss wrote: > Subject: Re: CCL:homology modeling boundary > > You might look at the rubredoxins, particularly Pyrococcus furiosus. The only > two references I can grap quickly are: > > Wampler et al. Protein Science, vol 2, pages 640-649 (1993) > Bradley et al. Protein Science vol 2, pages 650-665 (1993) > > I believe the structure of Pyrococcus furiosus has been determined by X-ray > recently but I can't find the reference. A quick check of the PDB should tell > if I am mistaken. > > Looking forward to a summary as I would like to present validations in our > molecular modeling class. > > -- > Jeff Nauss > > *********************************************************************** > * UU UU Jeffrey L. Nauss, PhD * > * UU UU Director, Molecular Modeling Services * > * UU UU Department of Chemistry * > * UU UU CCCCCCC University of Cincinnati * > * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * > * UUUU CC * > * CC Telephone: 513-556-0148 Fax: 513-556-9239 * > * CC * > * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * > * CCCCCCC URL http://www.che.uc.edu/~nauss * > *********************************************************************** On Sep 12, 9:35am, Dick Swenson wrote: > Subject: Comp Chem Responses > Hello, > > I noted your recent query to the Computational Chemistry e-mailer regarding > the validation of homology models. You might check out the following reference > > Harrison, R.W., D. Chatterjee, and I.T. Weber. 1995. Analysis of six protein > structures predicted by comparative modeling techniques. Proteins 23:463-471. > > > Also, I have an interest in this area and would very much like to receive a > summary of any responses you get back. > > Thanks and good luck, > > Richard P. Swenson, Ph.D. > > *********************************************************************** > * Richard P. Swenson | ..... ..... . . * > * Dept of Biochemistry | Tel: 614-292-9428 . . . . . * > * Ohio State University | FAX: 614-292-6773 . . ..... . . * > * 484 West 12th Avenue | Swenson.1@osu.edu . . . . . * > * Columbus, OH 43210 | ..... .... ..... * > *********************************************************************** On Sep 12, 2:00pm, Peter Grootenhuis wrote: > Subject: homology model /xray > Dear Fabrice, we published a paper in this area in which we made a comparison > on thrombin: > Koymans, L. M. H.; Grootenhuis, P. D. J.; Haasnoot, C. A. G. > "Homology Model-building of Human Thrombin: Optimisation of Modelling > Protocol and Comparison With X-ray Structure" > Recl. Trav. Chim. Pays-Bas 1993, 112, 161-168. > Also check-out the recent paper of Moult in Curr Opin. Biotechnol. on this > subject > > Peter Grootenhuis > ______________________________________________________________________________ > Dr. Peter D.J. Grootenhuis | > N.V. Organon / CMC Dept. RK2337 | Phone : +31-412-661920 > P.O. Box 20 / 5340 BH Oss | Fax : +31-412-662539 > The Netherlands | E-mail : p.grootenhuis@organon.akzonobel.nl > _________________________________|____________________________________________ On Sep 13, 4:40pm, Vidana C. Epa wrote: > Subject: Re: CCL:homology modeling > Hi Fabrice, > > See for example "A critical assessment of comparative molecular > modeling of tertiary structures of proteins" by S. Mosimann et al. in > Proteins, vol. 23, 301(1995). However, they don't relate the relative > success of any of the methods to any "superiority" of one method over > another. > > Cheers, > > Vidana C. Epa > > Biomolecular Research Institute, > 343 Royal Parade, > Parkville, Vic. 3052, > AUSTRALIA. > > > Tel: (61) - 3 - 9342 - 4300 > Fax: (61) - 3 - 9342 - 4301 > > email: vepa@tigger.mel.dbe.csiro.au > On Sep 13, 1:43pm, Mark J Forster wrote: > Subject: validation of homology modeling > > Fabrice > > Point your WWW browser to the results of the 1994 meeting on the > critical assessment of structure prediction (CASP) meeting. > http://www-bio.llnl.gov/bbrp/structural_bio/asilomar/Meeting.desc.text.html > > and see details of the upcoming CASP2 meeting > > http://iris4.carb.nist.gov/casp2/ > > > Best Wishes > > Mark J Forster > Manager Protein Applications Product Development > Molecular Simulations Inc. > 9685 Scranton Rd, > San Diego, CA 92121, USA. > Phone (619) 458 9990 > FAX (619) 458 0136 > e-mail: mjf@msi.com > WWW: http://www.msi.com/ On Sep 12, 2:12pm, Fabrice Leclerc wrote: > Subject: The current state of the art in protein structure prediction > > > > John Moult: The current state of the art in protein structure > > prediction [Review article] Current Opinion in Biotechnology 1996 7 : > > 422-427. > > > > Abstract > > The capabilities of current protein structure prediction methods have > > been assessed from the outcome of a set of blind tests. In comparative > > modeling, many of the numerical methods did not perform as well as > > expected, although the resulting structures are still of great > > practical use. The new methods of fold identification ('threading') > > were partially successful, and show considerable promise for the > > future. Except for secondary structure data, results from traditional > > ab initio methods were poor. A second blind prediction experiment is > > underway, and progress in all areas is expected. > > > > ---------------------------------------------------------------------- > > * As a registered member of BioMedNet you may read this article now > > [Full text] > > ---------------------------------------------------------------------- > > > > Electronic Press / biomednet@cursci.co.uk > http://BioMedNet.com/cgi-bin/members1/abstract.pl?bt7413 **********************************End of summary******************************* From zhorton@sundsu1.deltast.edu Tue Sep 17 13:12:26 1996 Received: from dsu.deltast.edu for zhorton@sundsu1.deltast.edu by www.ccl.net (8.7.5/950822.1) id MAA15622; Tue, 17 Sep 1996 12:10:24 -0400 (EDT) Received: from sundsu1.deltast.edu by dsu.deltast.edu (AIX 3.2/UCB 5.64/4.03) id AA33627; Tue, 17 Sep 1996 11:08:19 -0500 Received: by sundsu1.deltast.edu (4.1/SMI-4.1) id AA04573; Tue, 17 Sep 96 11:03:09 CDT Date: Tue, 17 Sep 1996 11:03:08 -0500 (CDT) From: Heather Horton To: CHEMISTRY@www.ccl.net Subject: Gaussian Z-Matrices Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters! My evil boss gave me the assignment of calculating points with Gaussian 94, but I don't have the manual! I created the Z matrix for CH4 and NH3 on my own and ran them. Here is a listing of the partial output: For CH4 I got -- ************************************************** Gaussian 94: CrayXMP-Unicos-G94RevD.3 1-May-1996 22-Jul-1996 ************************************************** %chk=ch4 ----------------- #RHF/6-31G** Test ----------------- 1/38=1/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,7=101,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,19=1,28=1/1; 99/5=1,9=1/99; ---------------------------- Single point CH4 calculation ---------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C H 1 RCH1 H 1 RCH2 2 DTET H 1 RCH3 2 DTET 3 DIHE 0 H 1 RCH4 2 DTET 3 -DIHE 0 Variables: RCH1 1. RCH2 1. RCH3 1. RCH4 1.25 DIHE 120. DTET 109.5 ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 C 2 2 H 1 1.000000( 1) 3 3 H 1 1.000000( 2) 2 109.500( 5) 4 4 H 1 1.000000( 3) 2 109.500( 6) 3 120.000( 8) 0 5 5 H 1 1.250000( 4) 2 109.500( 7) 3 -120.000( 9) 0 ------------------------------------------------------------------------ Z-Matrix orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 0.000000 0.000000 0.000000 2 1 0.000000 0.000000 1.000000 3 1 0.942641 0.000000 -0.333807 4 1 -0.471321 -0.816351 -0.333807 5 1 -0.589151 1.020439 -0.417259 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.000000 0.000000 3 H 1.000000 1.633283 0.000000 4 H 1.000000 1.633283 1.632703 0.000000 5 H 1.250000 1.843100 1.842457 1.842457 0.000000 Interatomic angles: H2-C1-H3=109.5 H2-C1-H4=109.5 H3-C1-H4=109.4424 H2-C1-H5=109.5 H3-C1-H5=109.4424 H4-C1-H5=109.4424 Stoichiometry CH4 Framework group CS[SG(CH2),X(H2)] Deg. of freedom 6 Full point group CS NOp 2 Largest Abelian subgroup CS NOp 2 Largest concise Abelian subgroup CS NOp 2 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 0.000000 0.025048 0.000000 2 1 0.940843 0.363889 0.000000 3 1 -0.473763 0.355379 0.816351 4 1 -0.473763 0.355379 -0.816351 5 1 0.006683 -1.224934 0.000000 ---------------------------------------------------------- And, for NH3 I got -- ************************************************** Gaussian 94: CrayXMP-Unicos-G94RevD.3 1-May-1996 30-Jun-1996 ************************************************** %chk=nh3 ----------------- #RHF/6-31G** Test ----------------- 1/38=1/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,7=101,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,19=1,28=1/1; 99/5=1,9=1/99; ---------------------------- Single point NH3 calculation ---------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 N X1 N RX H1 N RNH X1 DUMB H2 N RNH X1 DUMB H1 DIHE 0 H3 N RNH X1 DUMB H1 -DIHE 0 Variables: RX 1.02 RNH 1.02 DIHE 120. DUMB 108. ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 N 2 X 1 1.020000( 1) 3 2 H 1 1.020000( 2) 2 108.000( 5) 4 3 H 1 1.020000( 3) 2 108.000( 6) 3 120.000( 8) 0 5 4 H 1 1.020000( 4) 2 108.000( 7) 3 -120.000( 9) 0 ------------------------------------------------------------------------ Z-Matrix orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 7 0.000000 0.000000 0.000000 2 -1 0.000000 0.000000 1.020000 3 1 0.970078 0.000000 -0.315197 4 1 -0.485039 -0.840112 -0.315197 5 1 -0.485039 0.840112 -0.315197 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 N 0.000000 2 X 1.020000 0.000000 3 H 1.020000 1.650395 0.000000 4 H 1.020000 1.650395 1.680224 0.000000 5 H 1.020000 1.650395 1.680224 1.680224 0.000000 Interatomic angles: X2-N1-H3=108. X2-N1-H4=108. H3-N1-H4=110.9015 X2-N1-H5=108. H3-N1-H5=110.9015 H4-N1-H5=110.9015 Stoichiometry H3N Framework group C3V[C3(N),3SGV(H)] Deg. of freedom 2 Full point group C3V NOp 6 Largest Abelian subgroup CS NOp 2 Largest concise Abelian subgroup CS NOp 2 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 7 0.000000 0.000000 0.094559 2 1 0.000000 0.970078 -0.220638 3 1 0.840112 -0.485039 -0.220638 4 1 -0.840112 -0.485039 -0.220638 ---------------------------------------------------------- I have two questions about these: (1) First, how do I change the input so I can run multiple geometries at once? For example, I would like to change a bond length from 0.8 Angstroms to 1.6 Angstroms in increments of 0.1 Angstroms? (2) I ran these SYMMETRIC cases for CH4 and NH3 to see if my input deck was correct? But, I was surprised to see that when Gaussian 94 calculated the Interatomic angles they didn't have the symmetry I expected. Notice in NH3 that the H-N-H bond angles are not 111 degrees like I had expected. Am I misunderstanding this? Thanks everybody, HH p.s. shouldn't these last 2 H-C-H bond angles for CH4 be 109.5 too??? H2-C1-H5=109.5 H3-C1-H5=109.4424 H4-C1-H5=109.4424 From zhorton@sundsu1.deltast.edu Tue Sep 17 14:05:38 1996 Received: from dsu.deltast.edu for zhorton@sundsu1.deltast.edu by www.ccl.net (8.7.5/950822.1) id MAA15692; Tue, 17 Sep 1996 12:35:50 -0400 (EDT) Received: from sundsu1.deltast.edu by dsu.deltast.edu (AIX 3.2/UCB 5.64/4.03) id AA33627; Tue, 17 Sep 1996 11:08:19 -0500 Received: by sundsu1.deltast.edu (4.1/SMI-4.1) id AA04573; Tue, 17 Sep 96 11:03:09 CDT Date: Tue, 17 Sep 1996 11:03:08 -0500 (CDT) From: Heather Horton To: CHEMISTRY@www.ccl.net Subject: Gaussian Z-Matrices Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters! My evil boss gave me the assignment of calculating points with Gaussian 94, but I don't have the manual! I created the Z matrix for CH4 and NH3 on my own and ran them. Here is a listing of the partial output: For CH4 I got -- ************************************************** Gaussian 94: CrayXMP-Unicos-G94RevD.3 1-May-1996 22-Jul-1996 ************************************************** %chk=ch4 ----------------- #RHF/6-31G** Test ----------------- 1/38=1/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,7=101,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,19=1,28=1/1; 99/5=1,9=1/99; ---------------------------- Single point CH4 calculation ---------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C H 1 RCH1 H 1 RCH2 2 DTET H 1 RCH3 2 DTET 3 DIHE 0 H 1 RCH4 2 DTET 3 -DIHE 0 Variables: RCH1 1. RCH2 1. RCH3 1. RCH4 1.25 DIHE 120. DTET 109.5 ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 C 2 2 H 1 1.000000( 1) 3 3 H 1 1.000000( 2) 2 109.500( 5) 4 4 H 1 1.000000( 3) 2 109.500( 6) 3 120.000( 8) 0 5 5 H 1 1.250000( 4) 2 109.500( 7) 3 -120.000( 9) 0 ------------------------------------------------------------------------ Z-Matrix orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 0.000000 0.000000 0.000000 2 1 0.000000 0.000000 1.000000 3 1 0.942641 0.000000 -0.333807 4 1 -0.471321 -0.816351 -0.333807 5 1 -0.589151 1.020439 -0.417259 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.000000 0.000000 3 H 1.000000 1.633283 0.000000 4 H 1.000000 1.633283 1.632703 0.000000 5 H 1.250000 1.843100 1.842457 1.842457 0.000000 Interatomic angles: H2-C1-H3=109.5 H2-C1-H4=109.5 H3-C1-H4=109.4424 H2-C1-H5=109.5 H3-C1-H5=109.4424 H4-C1-H5=109.4424 Stoichiometry CH4 Framework group CS[SG(CH2),X(H2)] Deg. of freedom 6 Full point group CS NOp 2 Largest Abelian subgroup CS NOp 2 Largest concise Abelian subgroup CS NOp 2 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 6 0.000000 0.025048 0.000000 2 1 0.940843 0.363889 0.000000 3 1 -0.473763 0.355379 0.816351 4 1 -0.473763 0.355379 -0.816351 5 1 0.006683 -1.224934 0.000000 ---------------------------------------------------------- And, for NH3 I got -- ************************************************** Gaussian 94: CrayXMP-Unicos-G94RevD.3 1-May-1996 30-Jun-1996 ************************************************** %chk=nh3 ----------------- #RHF/6-31G** Test ----------------- 1/38=1/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,7=101,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,19=1,28=1/1; 99/5=1,9=1/99; ---------------------------- Single point NH3 calculation ---------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 N X1 N RX H1 N RNH X1 DUMB H2 N RNH X1 DUMB H1 DIHE 0 H3 N RNH X1 DUMB H1 -DIHE 0 Variables: RX 1.02 RNH 1.02 DIHE 120. DUMB 108. ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 N 2 X 1 1.020000( 1) 3 2 H 1 1.020000( 2) 2 108.000( 5) 4 3 H 1 1.020000( 3) 2 108.000( 6) 3 120.000( 8) 0 5 4 H 1 1.020000( 4) 2 108.000( 7) 3 -120.000( 9) 0 ------------------------------------------------------------------------ Z-Matrix orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 7 0.000000 0.000000 0.000000 2 -1 0.000000 0.000000 1.020000 3 1 0.970078 0.000000 -0.315197 4 1 -0.485039 -0.840112 -0.315197 5 1 -0.485039 0.840112 -0.315197 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 N 0.000000 2 X 1.020000 0.000000 3 H 1.020000 1.650395 0.000000 4 H 1.020000 1.650395 1.680224 0.000000 5 H 1.020000 1.650395 1.680224 1.680224 0.000000 Interatomic angles: X2-N1-H3=108. X2-N1-H4=108. H3-N1-H4=110.9015 X2-N1-H5=108. H3-N1-H5=110.9015 H4-N1-H5=110.9015 Stoichiometry H3N Framework group C3V[C3(N),3SGV(H)] Deg. of freedom 2 Full point group C3V NOp 6 Largest Abelian subgroup CS NOp 2 Largest concise Abelian subgroup CS NOp 2 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 7 0.000000 0.000000 0.094559 2 1 0.000000 0.970078 -0.220638 3 1 0.840112 -0.485039 -0.220638 4 1 -0.840112 -0.485039 -0.220638 ---------------------------------------------------------- I have two questions about these: (1) First, how do I change the input so I can run multiple geometries at once? For example, I would like to change a bond length from 0.8 Angstroms to 1.6 Angstroms in increments of 0.1 Angstroms? (2) I ran these SYMMETRIC cases for CH4 and NH3 to see if my input deck was correct? But, I was surprised to see that when Gaussian 94 calculated the Interatomic angles they didn't have the symmetry I expected. Notice in NH3 that the H-N-H bond angles are not 111 degrees like I had expected. Am I misunderstanding this? Thanks everybody, HH p.s. shouldn't these last 2 H-C-H bond angles for CH4 be 109.5 too??? H2-C1-H5=109.5 H3-C1-H5=109.4424 H4-C1-H5=109.4424 From owner-chemistry@ccl.net Tue Sep 17 21:12:21 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id UAA18008; Tue, 17 Sep 1996 20:32:38 -0400 (EDT) Received: from bioc1.msi.com for dgregory@msi.com by bedrock.ccl.net (8.7.5/950822.1) id UAA09721; Tue, 17 Sep 1996 20:32:35 -0400 (EDT) Received: from biff.msi.com by bioc1.msi.com (5.64/0.0) id AA06527; Tue, 17 Sep 96 17:32:06 -0700 Received: from [146.202.16.3] by biff.biosym.com (4.1/SMI-4.1) id AA21037; Tue, 17 Sep 96 17:32:03 PDT X-Sender: dgregory@146.202.0.225 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 17 Sep 1996 17:32:59 -0700 To: mathog@seqaxp.bio.caltech.edu From: dgregory@msi.com (Don Gregory) Subject: Re: Molecular Modeling programs on different platforms - table correct? Cc: chemistry@ccl.net (Comp. Chem. List) Hi David, I'd like to encourage you in two respects, first if you could change the company name, in your tables, from Biosym to MSI ..... secondly, I'd suggest you check out the WebLab viewer that we're now offering freely, on Windows-NT, -95, PowerMac and Macintosh Anyone can grab it at www.msi.com There are also forms based pages that allow for feedback. DG > >mathog@seqaxp.bio.caltech.edu wrote: >> >> Hi, >> >> Periodically I check the status of various molecular modeling/molecular >> display/related programs with respect to portability. This is my latest >> table - if anybody sees any errors or wants to add something, please chime >> in. >> >> Listed alphabetically >> >> MIPS ---DEC Alpha---- Intel >> What SGI DU WNT Windows GraphicsType >> >> Biosym Yes No* No* No* GL >> Grasp Yes No No No GL >> MidasPlus Yes No No No GL >> molmol Yes Yes No No X11 >> O Yes No No No GL >> rasmol Yes Yes ? Yes X11/Windows >> Setor Yes No No No GL >> VMD Yes No No No GL >> XtalView Yes Yes No No GL/X11 >> >> * Separately licensed "Axxess" product lets Biosym run as an X11 client. >> >> Kind of amazing to me that more of these have not been ported to other >> platforms, for instance Alpha/Linux or WNT. Looks like the only really >> portable one is Rasmol. In terms of horsepower the SGIs are at least twice >> as expensive as these alternatives. I guess the ports will only come when >> the grants start coming back marked with "buy cheaper platforms". >> >> If I get a vote, I cast it for moving to WNT. Not that I'm a big fan of >> that OS, but realistically, WNT workstations would be a lot more readily >> accepted by our undergrads then the current set of SGIs are, and getting >> other software for WNT machines (word processors and so forth) would be one >> heck of a lot easier and lots cheaper than it is for SGIs. >> >> Regards, >> >> David Mathog >> mathog@seqaxp.bio.caltech.edu >> Manager, sequence analysis facility, biology division, Caltech > Dr. Don Gregory (dgregory@msi.com) Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com