From tamasgunda@tigris.klte.hu Thu Oct 26 03:59:28 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id DAA19653; Thu, 26 Oct 1995 03:47:36 -0400 Message-Id: <199510260747.DAA19653@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Thu, 26 Oct 1995 08:47:56 EDT Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Thu, 26 Oct 1995 08:47:57 +1 Subject: distance from plane Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Istvan Enyedy wrote: > > I am looking for a program wich have the following features: > - can calculate the equation of the plane defined by the coordinates of 3 > atoms; > - can find the distance from an atom to the plane defined above; > - the program runs on PC or Macintosh. > > Thanks for every help. > > Istvan Enyedy > istvan@bioorg.ee.cua.edu The program Mol2Mol for Windows can do this: distance of an atom from the plane or centroid of other atoms, or two planes selected by 3-3 atoms (e.g. two phenyl rings), and the program calculates the dihedral angle. Forthcoming version of Mol2mol will do it with two fitted planes too. ------------------------------------------------------------------ MOL2MOL -- an easy-to-use file conversion program for the chemist. Mol2Mol automatically converts many of the widely used file formats in chemistry. Running under Windows, Mol2Mol helps you with the conversion, manipulation and inspection of different molecular structure files. Currently over twenty different molecule file formats are supported, as well as your own free format ASCII files. Mol2Mol automatically recognizes the format of most of these files. The program also helps in capturing co-ordinates from the big output files of quantum chemistry programs. It possesses some chemical intelligence for recognizing extended atom and bond types, chemical environments, which is necessary for converting simpler formats to SYBYL, HyperChem or PCMODEL files, for example. Mol2Mol is more than just a file conversion system. It has a number of features which offer outstanding ease-of-use to a researcher who needs different tools for file conversion and molecule inspection. * Graphical window to inspect the input molecule with standard manipulations (translation, rotation, stereo modes etc.) * Quick calculation of basic geometrical data (distances, angles, planes, pyramidality, proton-proton and proton-methyl centroid distances, distance from fitted planes etc) * Simple correction of atom or bond types * In the case of problems an ASCII editor for manual corrections of input or output file * Batch process for files of similar type * Text window to follow the conversion process. For the time being, MOL2MOL can automatically recognize (R) and write (W) the following co-ordinate file formats: ALCHEMY I-III *RW SYBYL MOL and MOL2 *RW CPSS, ISIS mol *RW MOLIDEA *RW Desktop Molecular Modeller *RW PCMODEL *RW HyperChem *RW MOBY (Cartesian) *RW Beilstein Rosdal *R ChemDraft (Cartesian) *RW ChemWindow (mol) *RW Brookhaven PDB *RW Z matrix, free format #*RW AMPAC *RW MOPAC *RW X-ray fractional CIF *R Cambridge FDAT *R Cambridge MODEL *R user's free format #R Cartesian free format #R PLUTO W PLT W WIMP (.ftr) W Schakal W * recognized automatically # insertion of a marker is necessary when capturing co-ordinates Since many of the above programs are also capable of communicating with others or accepting different database formats (e.g. Protein Data Bank, CSSR files), the effective range of MOL2MOL is even wider. Several programs not included in the above table use common formats (ChemDraw, ChemX, MPG, Insight, etc.). MOL2MOL will continue to be developed to accept or write new file formats (MacroModel, MDL V3000, Insight, ChemDr System requirements: IBM PC with Windows 3.1, 4 MB RAM, maths coprocessor. For more information contact: Cherwell Scientific Publ .Ltd The Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA Tel: +44 (0)1865 784800 Fax: +44 (0)1865 784801 e-mail: info@cherwell.com mol2mol@cherwell.com or w3: http://www.cherwell.com/products/mol2mol ------------------------------------------------------- ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From neum@cma.univie.ac.at Thu Oct 26 06:59:32 1995 Received: from homer.cma.univie.ac.at for neum@cma.univie.ac.at by www.ccl.net (8.6.10/950822.1) id GAA21642; Thu, 26 Oct 1995 06:50:17 -0400 Received: by homer.cma.univie.ac.at; (5.65/1.1.8.2/12Jan95-0202PM) id AA29292; Thu, 26 Oct 1995 11:54:25 +0100 Date: Thu, 26 Oct 1995 11:54:25 +0100 From: Arnold Neumaier Message-Id: <9510261054.AA29292@homer.cma.univie.ac.at> To: chemistry@www.ccl.net Subject: Re: CCL:Best Fitting Algorithms Cc: erich@tbi.univie.ac.at, neum@cma.univie.ac.at >>I'm interested in your opinions about various best fitting algorithms for non-linear optimization. Output of my program (an electrochemical simulator) is a wave (couple of calculated points) which must be compared with experimental data.<< you can get a least squares code for data fitting in fortran77 by sending an email with body send nsf.f from port to netlib@nac.no or to any other netlib site (add the line send index to get more info about netlib). nsf.f minimizes the sum of squares of a vector-valued function, using function values only, and hence is well-suited to your purpose. Usually, it is much faster than simplex-like methods. ---------------------------------------------------- Prof. Dr. Arnold Neumaier Institut fuer Mathematik Universitaet Wien Strudlhofgasse 4 A-1090 Wien Austria Tel: +431 407 63632 (new!) FAX: +431 31367 4040 email: neum@cma.univie.ac.at www: http://solon.cma.univie.ac.at/~neum/ ---------------------------------------------------- From polowin@hyper.hyper.com Thu Oct 26 10:42:30 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/950822.1) id KAA26625; Thu, 26 Oct 1995 10:42:20 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.9/8.6.9) with SMTP id KAA02083 for <@www.hyper.com:CHEMISTRY@www.ccl.net>; Thu, 26 Oct 1995 10:50:54 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@www.ccl.net id AA01978; Thu, 26 Oct 95 10:50:52 -0400 Date: Thu, 26 Oct 95 10:50:52 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9510261450.AA01978@hyper.hyper.com> To: CHEMISTRY@www.ccl.net Subject: HyperChem 4.5 for SGI We are pleased to announce the release of HyperChem 4.5 for Silicon Graphics Workstations. HyperChem is an integrated and flexible molecular modeling product for chemists. It is a powerful package with capabilities for visualizing, analyzing, and simulating molecules, and for communicating information about molecular structures. Running on Silicon Graphics computers, HyperChem is an affordable tool that makes computer simulation more accessible to researchers and to educators. HyperChem can provide valuable insight into molecular structure, flexibity, and properties. You can compute heats of formation, ionization potentials, electron affinities, dipole moments, as well as UV-visible and IR spectra. HyperChem integrates easily with scientific and business productivity software and chemical databases. HyperChem 4.5 includes molecular modelling, semi-empirical, and _ab initio_ calculations. A demo version of the software, and the tutorial manual in PostScript format, are available from the Conputational Chemistry archives on www.ccl.net, in the directory /pub/chemistry/software/SGI/HyperChem-demo . The demo software is the complete working package but the license is limited to one month of use. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From polowin@hyper.hyper.com Thu Oct 26 11:52:49 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/950822.1) id LAA28512; Thu, 26 Oct 1995 11:52:42 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.9/8.6.9) with SMTP id LAA02321; Thu, 26 Oct 1995 11:58:44 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:94970459@vax1.dcu.ie id AA02784; Thu, 26 Oct 95 11:58:37 -0400 Date: Thu, 26 Oct 95 11:58:37 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9510261558.AA02784@hyper.hyper.com> To: Paddy Kane <94970459@vax1.dcu.ie> Subject: Re: CCL:semi-empirical methods Cc: CHEMISTRY@www.ccl.net, hyperchem@hyper.com > Date: Tue, 24 Oct 1995 10:59:15 +0000 (GMT) > From: Paddy Kane <94970459@vax1.dcu.ie> > Calculation of heat of formation of benzoic acid > delta Hf/(kcal/mol) > AM1 -54.1467462 > PM3 -53.6776001 > ZINDO/1 -3117.2768454 > ZINDO/S -5062.7571910 > > Calculation of heat of formation of cyclopentanone > delta Hf/(kcal/mol) > AM1 -52.5334612 > PM3 -53.1513803 > ZINDO/1 -2586.4691313 > ZINDO/S -4012.5111479 > > 1) The HyperChem Computational Chemistry manual quotes values of > -70.1 kcal/mol and -46.0 kcal/mol for the enthalpy of formation of benzoic > acid and cyclopentanone respectively. So how accurate can we expect > Hyperchem's semiempirical methods to be? As has been stated here before, several times and recently -- we can expect HyperChem's calculations to be *exactly* as accurate as the same calculations performed by other software. We use published methods with standard parameters; we have not had any reports of our results differing from the results of others' calculations that did not turn out to be because of differences in the options selected or in the structure being calculated. My calculations with HyperChem for benzoic acid gave heats of formation of -68.1 kcal/mol for AM1, -66.4 kcal/mol for PM3, and -3147.6 kcal/mol for ZINDO/1. ZINDO/S did not converge. The AM1 and PM3 results are consistent with literature values for those calculations. (See J.J. Stewart, _J. Computer-Aided Mol. Design_ *4*, 1-105 (1990).) The ZINDO methods do not reproduce heats of formation well. My results for cyclopentanone are: -55.5 kcal/mol for AM1, -55.3 kcal/mol for PM3, -2608.3 for ZINDO/1, and no convergence for ZINDO/S. The Stewart article gives -36.1 kcal/mol as the heat of formation calculated with AM1 with MOPAC, but our repetition of that calculation with AM1 with MOPAC gives -55.3 kcal/mol. This appears to be an error in the article (and in our manual, which quotes results from the article). > 2) Why are the ZINDO/1 and ZINDO/S methods giving me such apparently > incorrect values? The ZINDO methods weren't parameterized by fitting to experimental heats of formation. ZINDO/S was optimized to give good electronic transition (UV/visible) results. > 3) Another question (apparently unrelated to the first two questions) is > why the following message appeared in my log file for calcium but not for > magnesium in the ZINDO/1 calculations on the calixarene complexes: > WARNING message received from node=0: > Atom 221 with atomic number 20 the value of bonding parameter of s orbital > is less than or equal to zero, please check your parameter file zindo1_1.abp. The s and p bonding parameters for Ca are actually negative, unlike those parameters for all of the other atoms. Usually, for those parameters to be negative would indicate an error in the parameter set, so HyperChem is warning you of a possible problem. In this case, you should ignore the warning and continue the calculation. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From martin.norin@sto.pharmacia.se Thu Oct 26 18:29:39 1995 Received: from gatekeeper.pharmacia.se for martin.norin@sto.pharmacia.se by www.ccl.net (8.6.10/950822.1) id SAA10590; Thu, 26 Oct 1995 18:17:38 -0400 Received: from mailgate.pharmacia.se by gatekeeper.pharmacia.se; (5.65/1.1.8.2/16Feb95/sal) id AA19739; Thu, 26 Oct 1995 23:22:47 +0100 Received: by mailgate.pharmacia.se (5.65/DEC-Ultrix/4.3/sal-950131) id AA14408; Thu, 26 Oct 1995 23:13:06 +0100 Date: Thu, 26 Oct 1995 23:13:06 +0100 Received: from umc by mailgate.pharmacia.se via MR/PHAROS with conversational-MRIF; Thu, 26 Oct 95 23:13:05 +0100 Posted: Thu, 26 Oct 95 23:13:41 +0100 Sender: martin.norin@sto.pharmacia.se From: "NOYM" Message-Id: <4841132326101995/A23911/MEANIE> App-Message-Id: <4841132326101995/A23911/MEANIE/119AD5CD2000> To: chemistry@www.ccl.net Subject: Compressed PDB list. Sensitivity: Company-Confidential Dear Colleagues, The PDB directory currently consists of about 3800 records. However, many of these are different versions of the same structures (for example different mutants of the same protein or one protein with a a number of different ligands or a lot of DNA/RNA structures). It would, for a number of reasons, be very valuable to have a subset of the PDB containing representatives ("the best structure") of each unique protein, and important conformers. If anybody have done a comprehensive investigation to compile such a list or if it is already available on the net please let me now ! I'm also interrested in any hints how to do this without manually going through every record in the PDB. Of course I'll distribute a summary to the net ! Greetings, Martin Norin Pharmacia Biopharmaceuticals Stockholm, Sweden e-mail: martin.norin@sto.pharmacia.se From gford@post.smu.edu Thu Oct 26 19:14:40 1995 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.6.10/950822.1) id TAA11498; Thu, 26 Oct 1995 19:06:27 -0400 Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.1) id ; Thu, 26 Oct 95 18:06 CDT Message-Id: Date: Thu, 26 Oct 95 18:06 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: CCL: ZINDO "Heats of formation" Joel Polowin writes: > My calculations with HyperChem for benzoic acid gave heats of formation of > -68.1 kcal/mol for AM1, -66.4 kcal/mol for PM3, and -3147.6 kcal/mol for > ZINDO/1. ZINDO/S did not converge. > > Why are the ZINDO/1 and ZINDO/S methods giving me such apparently > incorrect values? I am not a Hyperchem user, but surely the answer is that the ZINDO data are total energies, not heats of formation at all. George P. Ford ============================================================================ George P. Ford | email: gford@mail.smu.edu Department of Chemistry | telephone: (214)768-2479 Southern Methodist University | fax: (214)768-4089 Dallas, Texas 75275 | ============================================================================ From cory@bohr.chem.mun.ca Thu Oct 26 20:59:41 1995 Received: from piva.ucs.mun.ca for cory@bohr.chem.mun.ca by www.ccl.net (8.6.10/950822.1) id UAA13147; Thu, 26 Oct 1995 20:56:08 -0400 Received: from bohr.chem.mun.ca (bohr.chem.mun.ca [134.153.14.2]) by piva.ucs.mun.ca (8.6.12/8.6.9) with SMTP id WAA04746 for <@morgan.ucs.mun.ca:CHEMISTRY@www.ccl.net>; Thu, 26 Oct 1995 22:26:05 -0230 Received: by bohr.chem.mun.ca (931110.SGI/921111.SGI.AUTO) for @morgan.ucs.mun.ca:CHEMISTRY@www.ccl.net id AA14634; Thu, 26 Oct 95 22:27:38 -0230 Date: Thu, 26 Oct 95 22:27:38 -0230 From: cory@bohr.chem.mun.ca (Cory C. Pye) Message-Id: <9510270057.AA14634@bohr.chem.mun.ca> To: CHEMISTRY@www.ccl.net Subject: Heats of Formation ZINDO/1 and ZINDO/S are obviously not working for H_f 's: This is either 1) poor parametrization of these for H_f's (probably not original intent) 2) these numbers are too 'small' to be the total energies which should be closer to the 1 million kcal order of magnitude (say near-HF or non-rel SWE) 3) the numbers might be the total 'valence' energy, but these would be even too small for these ( say near the 10^5 kcal magnitude 4) Could it be the use of a different reference state for the elements ( say C (g) at 298K instead of C(s) at 298K? The numbers seem to be in roughly the right ballpark for atomization. Although the parametrization may be poor, I wouldn't expect it to be THAT poor ( for heats of formation ) ************* ***************** ! Cory C. Pye *** ** ** ** ! Graduate Student ** * **** ! Unpaid Sys Admin ** * * ! Theoretical and ** * * ! Computational Chemistry *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) From mcgsw@cotton.vislab.olemiss.edu Thu Oct 26 22:29:43 1995 Received: from sun1.mcsr.olemiss.edu for mcgsw@cotton.vislab.olemiss.edu by www.ccl.net (8.6.10/950822.1) id WAA14148; Thu, 26 Oct 1995 22:21:14 -0400 Received: from cotton.vislab.olemiss.edu by sun1.mcsr.olemiss.edu (4.1/SMI-4.1) id AA04166; Thu, 26 Oct 95 21:24:41 CDT Received: by cotton.vislab.olemiss.edu (4.1/SMI-4.1) id AA20878; Thu, 26 Oct 95 21:21:04 CDT Date: Thu, 26 Oct 1995 21:21:02 -0500 (CDT) From: Scott Weston To: NOYM Cc: chemistry@www.ccl.net Subject: Re: CCL:Compressed PDB list. In-Reply-To: <4841132326101995/A23911/MEANIE> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Martin, I believe Chris Sander at EMBL has already done similar work (Hobohm & Sander, Protein Sci., 1994, 3:522-544) which should be accessible via the Net/Web at http://www.sander.embl-heidelberg.de. Good luck, Scott ================================================================= Scott Weston Lab Phone: (601) 232-7187 Grad. Student Lab FAX: (601) 232-5118 Dept. of Medicinal Chemistry Home Phone: (601) 234-0067 University of Mississippi mcgsw@cotton.vislab.olemiss.edu University, MS 38677 ================================================================= On Thu, 26 Oct 1995, NOYM wrote: > Dear Colleagues, > > The PDB directory currently consists of about 3800 records. However, many > of these are different versions of the same structures (for example different > mutants of the same protein or one protein with a a number of different ligands > or a lot of DNA/RNA structures). > > It would, for a number of reasons, be very valuable to have a subset of the > PDB containing representatives ("the best structure") of each unique protein, > and important conformers. > > If anybody have done a comprehensive investigation to compile such a list > or if it is already available on the net please let me now ! I'm also > interrested in any hints how to do this without manually going through every > record in the PDB. > > Of course I'll distribute a summary to the net ! > > Greetings, > Martin Norin > Pharmacia Biopharmaceuticals > Stockholm, Sweden > e-mail: martin.norin@sto.pharmacia.se > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: martin.norin@sto.pharmacia.se > -- Original Sender From: Address: martin.norin@sto.pharmacia.se > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From george@americium.mps.ohio-state.edu Thu Oct 26 23:14:43 1995 Received: from americium.mps.ohio-state.edu for george@americium.mps.ohio-state.edu by www.ccl.net (8.6.10/950822.1) id XAA14751; Thu, 26 Oct 1995 23:01:40 -0400 Received: by americium.mps.ohio-state.edu (IBM OS/2 SENDMAIL VERSION 1.3.2)/1.0) id AA0133; Thu, 26 Oct 95 22:58:38 -0400 Message-Id: <9510270258.AA0133@americium.mps.ohio-state.edu> Date: Fri, 27 Oct 95 3:58:38 +1900 From: George McBane Subject: React 3.21, DOS and OS/2 versions To: chemistry@www.ccl.net Cc: whitbeck1@llnl.gov (Mike Whitbeck) Reply-To: McBane.2@osu.edu X-Mailer: ELM [version 2.3 PL11] for OS/2 Hello all. I have posted DOS and OS/2 executable versions of Mike Whitbeck's React program, version 3.21 (current as of 10/20/95), to www.ccl.net. The program does numerical modeling of chemical kinetic systems, and can fit rate coefficients to experimental data. The programs are in pub/chemistry/software/MS-DOS/react and pub/chemistry/software/OS-2/react respectively. A simple manual and several example files are included. Both versions are in .zip format (Info-Zip style). These programs are identical in function to the original Macintosh version (also available at infomeister) as far as I know. Enjoy! -- George C. McBane mcbane.2@osu.edu Department of Chemistry The Ohio State University FAX (614) 292-1685 120 W. 18th Ave Columbus, OH 43210 Americium: atomic number 95, mp 994 C, bp 2607 C, d. 13.67 g/cc most easily prepared isotope mass 241, half-life 470 yr.