From owner-chemistry@ccl.net Tue Jul 4 12:54:30 1995 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.6.10/930601.1506) id MAA24539; Tue, 4 Jul 1995 12:44:44 -0400 Received: from hpf.ch.man.ac.uk (actually mchhpf.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Tue, 4 Jul 1995 17:44:34 +0100 From: Nathaniel (noj) Malcolm Message-Id: <17503.9507041643@hpf.ch.man.ac.uk> Subject: cation calcs To: chemistry@ccl.net Date: Tue, 4 Jul 95 17:43:53 BST Mailer: Elm [revision: 70.85] John Pollard wrote: >I was wondering what people thought about the most viable molecular orbital >approach to dealing with finding optimized geometries for +1 cations of >organic molecules. I have been just using UHF theory. Are there better >theories for dealing with these species? in response to thomas bally's response, there is also a CASSCF type mp2 correction available in Gaussian94 Mike Robbs OVB-MP2 code, you could try that. From owner-chemistry@ccl.net Tue Jul 4 13:39:30 1995 Received: from london.ks.uiuc.edu for bishop@london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id NAA25004; Tue, 4 Jul 1995 13:25:03 -0400 Received: from riga.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.16/16.2) id AA140328703; Tue, 4 Jul 1995 12:25:03 -0500 From: Tom Connor Bishop Message-Id: <199507041725.AA140328703@london.ks.uiuc.edu> Received: by riga.ks.uiuc.edu (NX5.67d/NX3.0X) id AA06373; Tue, 4 Jul 95 12:25:02 -0500 Date: Tue, 4 Jul 95 12:25:02 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY@ccl.net Subject: Announcing the Program NAMD, Version 1.0 Reply-To: bishop@london.ks.uiuc.edu Announcing the Program namd --------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability the program namd, a new package for high performance parallel molecular dynamics simulations. This software is being made available to the structural biology research community free of charge, and includes the source code for namd, documentation, and precompiled binaries for various parallel platforms The documentation, in postscript form, includes a programmers guide and a users guide. Obtaining namd ------------- A more complete description of namd is available via the namd WWW home page: http://www.ks.uiuc.edu:1250/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd Features -------- namd is a molecular dynamics program designed to provide high performance simulations for large biological molecular systems. Specifically, namd achieves high performance by exploiting the power of parallel computers and by providing a modular design that facilitates the implementation of new algorithms. A high degree of modularity is obtained by using an object-oriented design and implementation in C++. namd uses spatial decomposition coupled with a multithreaded, message-driven design, which provides a scalable, efficient parallel framework. namd also incorporates the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the Scientific Computing group at Duke University, which allows full electrostatic force evaluation in O(N) time. As part of the MDScope system, namd is connected via the communication system MDComm to the molecular graphics program VMD (also developed by the Theoretical Biophysics group) to provide such an interactive system where researchers can view and interact with a running simulation. The program has many features, which include: o Input and output file compatibility with X-PLOR o CHARMM19 and CHARMM22 parameter support o Support for traditional MD functions such as energy minimization, velocity rescaling, harmonic boundary conditions, harmonic atom restraints, etc. o Full electrostatic evaluation using DPMTA from Duke University integrated using a multiple timestep integration scheme. For more information on DPMTA, see the Scientific Computing home page at: http://www.ee.duke.edu/Research/SciComp.html o Spatial decomposition for O(N/P) scalability of memory, computation, and communication. o Message-driven, multithread design for high performance parallel execution. o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Portable parallelism provided by PVM and Charm++ communication systems o Integration with the program VMD, a molecular graphics program developed in the Theoretical Biophysics Group at the University of Illinois. See the VMD WWW home page for more info: http://www.ks.uiuc.edu:1250/Research/vmd VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communications package (called MDComm) constitute the 'MDScope' environment. Availability ------------ namd should run on any parallel platform with a C++ compiler and PVM version 3.3.6 or later. Tested Makefiles are included for clusters of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar. Precompiled binaries are provided for HP and SGI workstations. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation. From owner-chemistry@ccl.net Tue Jul 4 13:54:30 1995 Received: from london.ks.uiuc.edu for bishop@london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id NAA24989; Tue, 4 Jul 1995 13:24:49 -0400 Received: from riga.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.16/16.2) id AA140298689; Tue, 4 Jul 1995 12:24:50 -0500 From: Tom Connor Bishop Message-Id: <199507041724.AA140298689@london.ks.uiuc.edu> Received: by riga.ks.uiuc.edu (NX5.67d/NX3.0X) id AA06368; Tue, 4 Jul 95 12:24:49 -0500 Date: Tue, 4 Jul 95 12:24:49 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY@ccl.net Subject: Announcing the Program VMD, Version 1.0 Reply-To: bishop@london.ks.uiuc.edu Announcing the Program VMD, Version 1.0 --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.0 of the program VMD, a new package for the graphical display and visualization of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and a precompiled binary for Silicon Graphics workstations running version 5 or later of the IRIX operating system. The documentation, in postscript form, includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer such as Mosaic or Netscape. Obtaining VMD ------------- A more complete description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu:1250/Research/vmd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd (please see the README file in this directory for the latest version info) Features -------- VMD is designed for the visualization of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, and Raster3D. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu:1250/Research/namd VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ VMD runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library (a commercial port of the SGI GL library, available from Portable Graphics, Inc.) is available on your system. Two versions of the distribution are available, one including the complete VMD source code, and one which just includes a precompiled VMD executable for SGI IRIX version 5. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation. From owner-chemistry@ccl.net Tue Jul 4 15:28:44 1995 Received: from saguenay.IRO.UMontreal.CA for leclerc@IRO.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id PAA26364; Tue, 4 Jul 1995 15:28:44 -0400 Received: from lagrande.iro.umontreal.ca (lagrande.IRO.UMontreal.CA [132.204.32.32]) by saguenay.IRO.UMontreal.CA (8.6.12/8.6.12) with ESMTP id PAA29473 for ; Tue, 4 Jul 1995 15:28:38 -0400 Received: (from leclerc@localhost) by lagrande.iro.umontreal.ca (8.6.12/8.6.12) id PAA28407; Tue, 4 Jul 1995 15:28:37 -0400 Date: Tue, 4 Jul 1995 15:28:37 -0400 From: Fabrice Leclerc Message-Id: <199507041928.PAA28407@lagrande.iro.umontreal.ca> To: CHEMISTRY@ccl.net Subject: apramycin Hi, I'm looking for the coordinates of apramycin. Is there anybody that would know where I could get them. Thanks for your help. N.B.: there are 6 entries in the Cambridge Structural Database, but no coordinate information. regards, -- \ /\ \/ \______________________________________ /\ Fabrice Leclerc A--T Departement de Biochimie (----) Universite de Montreal G--C C.P. 6128, succ. Centre-Ville \/ Montreal, Quebec H3C 3J7 /\ Canada T--A tel. +1 (514)343-6111 poste 5354 (----) fax. +1 (514)343-2210 C--G leclerf@MEDCN.UMontreal.CA \/ leclerc@IRO.UMontreal.CA /\ _____________________________________ / \ / \/ From owner-chemistry@ccl.net Tue Jul 4 17:24:33 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id RAA27563; Tue, 4 Jul 1995 17:12:03 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id MAA07525; Tue, 4 Jul 1995 12:47:07 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:bouyer@ext.jussieu.fr id AA09368; Tue, 4 Jul 95 12:59:30 -0400 Date: Tue, 4 Jul 95 12:59:30 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9507041659.AA09368@hyper.hyper.com> To: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Re: MNDO/d softwares and sparkles Cc: chemistry@ccl.net, hyperchem@www.hyper.com > Date: Fri, 30 Jun 1995 08:58:01 +0100 > From: bouyer@ext.jussieu.fr (Frederic BOUYER) > Subject: MNDO/d softwares and sparkles > 2 - My problem is that counter-cations, like Na, ..., are taken into > account like sparkles; their charge is +1, ... . Is there a semi-empirical > program, or new parameters of Mopac, or new hamiltonians, that treat > correctly counter-cations? (except Hartree-Fock or DFT programs) HyperChem has Na parameters for the CNDO/INDO and ZINDO/1 methods. We'd be interested in pointers to published parameters for other methods. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.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 From owner-chemistry@ccl.net Tue Jul 4 23:09:37 1995 Received: from npd1.npd.ufpe.br for 64MNR@NPD.UFPE.BR by www.ccl.net (8.6.10/930601.1506) id WAA00961; Tue, 4 Jul 1995 22:47:25 -0400 From: <64MNR@NPD.UFPE.BR> Received: from NPD.UFPE.BR by NPD.UFPE.BR (PMDF V4.2-11 #6339) id <01HSHEZN07W08WXHKU@NPD.UFPE.BR>; Tue, 4 Jul 1995 19:23:32 -0300 Date: Tue, 04 Jul 1995 19:23:31 -0300 Subject: more information about d orbitals in tin complexes To: chemistry@ccl.net Message-id: <01HSHEZN10TU8WXHKU@NPD.UFPE.BR> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Joe Thank you for your response. I forgot to discriminate that I'm working with hexacoordinate tin complex so I need the inclusion of d orbitals. Does the new version of Hyperchem contain PM3 parameters with these orbitals? Some time ago one of our department requested information about how to buy this program and at moment we didn't have none information. Please, could you send us details about it. Regards, Bosco Bosco@vaxdqf.ufpe.br Joao Bosco P. da Silva Departamento de Quimica Fundamental CCEN - UFPE Cidade Universitaria - Recife - PE 50739 - Brasil