From gl@coil.mdy.univie.ac.at Wed Mar 29 02:24:36 1995 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.6.10/930601.1506) id CAA18264; Wed, 29 Mar 1995 02:19:38 -0500 Received: by coil.mdy.univie.ac.at (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA22112; Wed, 29 Mar 95 09:19:09 +0100 From: "Gerald Loeffler" Message-Id: <9503290919.ZM22110@coil.mdy.univie.ac.at> Date: Wed, 29 Mar 1995 09:19:07 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: Zn++ Coordinated by Cys or Cys- ? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi! Imagine Zn++ being coordinated by 3 Cys and 1 His in a Zinc Finger. Do you think it is likely that the Cys looses its S-bound proton (at neutral pH) because of the influence of the Zn++ ? This would mean, that the Zn++ is coordinated by 3 (negative) Cys- and 1 (neutral) His (the His holding a partial negative charge on one N). Thanx for your time and efforts, gerald P.S.: The pKa of Cys should be 8.5 ! -- Gerald Loeffler PhD student in Theoretical Biochemistry Email: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 Mail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria #include "fancy_ASCII_picture" #include "funny_statement" #include "standard_disclaimer" From howard_broughton@Merck.Com Wed Mar 29 07:09:38 1995 Received: from igw.merck.com for howard_broughton@Merck.Com by www.ccl.net (8.6.10/930601.1506) id HAA20630; Wed, 29 Mar 1995 07:03:25 -0500 Received: by igw.merck.com; Wed, 29 Mar 95 07:08:47 -0500 Message-Id: <9503291208.AA16471@igw.merck.com> Date: Wed, 29 Mar 1995 06:56:19 EST From: howard_broughton@merck.com (Howard Broughton) Subject: Want Program for Helical Wheel/string-of-beads To: CHEMISTRY@ccl.net Content-Type: TEXT/PLAIN Does anyone know of a program that will draw a "string of beads" and/or helical wheel representation of a helical or partly helical protein given just a primary sequence and helix end points? I'll summarize any responses. Many thanks, Howard_Broughton@merck.com From S.R.Kilvington@soton.ac.uk Wed Mar 29 08:09:39 1995 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.6.10/930601.1506) id HAA21082; Wed, 29 Mar 1995 07:57:38 -0500 Received: from vision.soton.ac.uk (vision.soton.ac.uk [152.78.128.74]) by beech.soton.ac.uk (8.6.10/hub-8.5) with ESMTP id NAA01139 for ; Wed, 29 Mar 1995 13:57:02 +0100 Received: (from srk@localhost) by vision.soton.ac.uk (8.6.10/client-8.6) id NAA22788 for CHEMISTRY@ccl.net; Wed, 29 Mar 1995 13:58:31 +0100 Message-Id: <199503291258.NAA22788@vision.soton.ac.uk> Subject: Ring perception algorithms To: CHEMISTRY@ccl.net Date: Wed, 29 Mar 1995 13:58:31 +0100 (BST) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 392 Dear all, does anyone have any references to ring perception algorithms? All I need to know is whether each bond in a molecule is either cyclic or acyclic. It's fairly easy to think of ways of doing it but I was wondering if there are any cunning tricks that have been developed that make it faster/use less memory etc. thanks for any help, Si. --- Simon Kilvington, srk@soton.ac.uk From mbdtsnm@hpf.ch.man.ac.uk Wed Mar 29 08:54:40 1995 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.6.10/930601.1506) id IAA21678; Wed, 29 Mar 1995 08:49:12 -0500 Received: from hpf.ch.man.ac.uk (actually mchhpf.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Wed, 29 Mar 1995 14:48:20 +0100 From: Nathaniel (noj) Malcolm Message-Id: <1905.9503291347@hpf.ch.man.ac.uk> Subject: solvent surface code To: chemistry@ccl.net Date: Wed, 29 Mar 95 14:47:59 BST Mailer: Elm [revision: 70.85] Does anyone have a program that will generate a set of equally spaced points (in xyz coordinates) on a surface of over-lapping spheres? If so i would be very interested,and will summarise any replies that i get for respondants. thank-you Noj Malcolm Noj.Malcolm@man.ac.uk From GAUSSIAN@cmchem.chem.cmu.edu Wed Mar 29 11:27:27 1995 Received: from cmchem.chem.cmu.edu for GAUSSIAN@cmchem.chem.cmu.edu by www.ccl.net (8.6.10/930601.1506) id LAA25310; Wed, 29 Mar 1995 11:21:31 -0500 From: Date: Wed, 29 Mar 1995 11:09:10 -0500 (EST) To: chemistry@ccl.net Message-Id: <950329110910.20200902@cmchem.chem.cmu.edu> Subject: Meet us in the DEC and IBM booths at ACS --------------------------------------------------------------------------- March 29, 1995 GAUSSIAN, INC. Carnegie Office Park Building 6 Pittsburgh, PA 15106 USA Phone - 412-279-6700 Fax - 412-279-2118 email - info@gaussian.com Representatives from Gaussian will be demonstrating in the Digital Equipment Corp. and IBM booths at the ACS Exposition in Anaheim, CA, April 3-5, 1995. We will be discussing the latest Gaussian features and also be demonstrating graphical interfaces to the program, including Cerius2 and Semichem. Be sure to stop by and say hello. --------------------------------------------------------------------------- This notice is sent without warranty of any kind, expressed or implied. Gaussian is a trademark of Gaussian, Inc. All other trademarks are the property of their respective holders. From marvin@iris131.biosym.com Wed Mar 29 12:39:46 1995 Received: from bioc1.biosym.com for marvin@iris131.biosym.com by www.ccl.net (8.6.10/930601.1506) id MAA26968; Wed, 29 Mar 1995 12:30:01 -0500 Received: from iris131.biosym.com by bioc1.biosym.com (5.64/0.0) id AA09019; Wed, 29 Mar 95 09:30:22 -0800 Received: by iris131.biosym.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id JAA14317; Wed, 29 Mar 1995 09:29:27 -0800 Date: Wed, 29 Mar 1995 09:29:27 -0800 From: marvin@biosym.com (Marvin Waldman) Message-Id: <199503291729.JAA14317@iris131.biosym.com> To: CHEMISTRY@ccl.net Subject: RE:Ring perception algorithms There are dozens (maybe hundreds) of papers in the chemical information literature on this subject. A recent paper on the topic with a rather clever new algorithm for this problem is: "Efficient Exact Solution of the Ring Perception Problem", R. Balducci and R.S. Pearlman, J. Chem. Inf. Comput. Sci., pp. 822-831, vol. 34, (1994). It has many references to earlier algorithms for dealing with ring perception. You will find that most of the effort in these algorithms is devoted to finding what is known as the SSSR which stands for Smallest Set of Smallest Rings. The problem of finding whether or not a bond is a ring bond is a much easier problem to solve which almost all of these algorithms do as part of their approach to finding the SSSR. An algorithm I found reasonably straightforward to implement and is also reasonably efficient with regard to locating all the ring bonds in the molecule in one pass through the connectivity tree is: "An Algorithm for the Perception of Synthetically Important Rings", J. Gasteiger and C. Jochum, J. Chem. Inf. Comput. Sci., pp. 43-48, vol. 19, (1978). Regards, Marvin Waldman, Ph.D. Director, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com From garciae@ucsub.colorado.edu Wed Mar 29 13:09:43 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.10/930601.1506) id MAA27622; Wed, 29 Mar 1995 12:57:10 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.11/8.6.9/CNS-3.5) id KAA22185; Wed, 29 Mar 1995 10:57:01 -0700 Date: Wed, 29 Mar 1995 10:57:00 -0700 (MST) From: Garcia Edgardo To: Simon Kilvington cc: CHEMISTRY@ccl.net Subject: Re: CCL:Ring perception algorithms In-Reply-To: <199503291258.NAA22788@vision.soton.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Simon, Yes, there are lots of ring-finding algortihms out there. Have a look at J.Chem.Inf.Comp.Sci. and Thetraedron Comp. Methodol. also at {Garcia E. & Reyes L.M.,J.Mol.Struct. Theochem, 282, 1993}, you will find an algorithm and references there. A simple way of doing it is : 1. Use a recursive prunning algorithm that cuts all terminal bonds. 2. The structure that remains has only ring and ring bridging bonds. 3. To know if a bond is a ring bond remove it and see if the molecule doesn't divide in two subunits. Now, depending on the complexity of your molecules, another way is obtaining the smallest set of rings (SSR). All bonds that are in this set are ring bonds. Hope this helps, Edgardo Garcia Cristol Chem. & Biochem. Univ. of Colorado BOULDER CO USA From HGF03236@niftyserve.or.jp Wed Mar 29 13:54:47 1995 Received: from inetnif.niftyserve.or.jp for HGF03236@niftyserve.or.jp by www.ccl.net (8.6.10/930601.1506) id NAA28308; Wed, 29 Mar 1995 13:40:18 -0500 Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id DAA11630; Thu, 30 Mar 1995 03:41:01 +0900 Message-Id: <199503291841.DAA11630@inetnif.niftyserve.or.jp> Date: Thu, 30 Mar 1995 03:38:00 +0900 From: =?ISO-2022-JP?B?GyRCQG44NkVEISFAY0knGyhC?= Subject: CCL:DV-X(alpha) program To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Dear netters! Where I can get DV-X(alpha) program? Thanks in advance. Y.Kawaharada Japan From richard@iris26.biosym.com Wed Mar 29 14:09:44 1995 Received: from bioc1.biosym.com for richard@iris26.biosym.com by www.ccl.net (8.6.10/930601.1506) id OAA28786; Wed, 29 Mar 1995 14:05:06 -0500 Received: from iris26.biosym.com by bioc1.biosym.com (5.64/0.0) id AA10794; Wed, 29 Mar 95 11:05:18 -0800 Received: by iris26.biosym.com via SMTP (931110.SGI/930416.SGI) for @bioc1.biosym.com:mbdtsnm@mchhpf.ch.man.ac.uk id AA23877; Wed, 29 Mar 95 11:04:23 -0800 Message-Id: <9503291904.AA23877@iris26.biosym.com> To: chemistry@ccl.net, mbdtsnm@mchhpf.ch.man.ac.uk Subject: Re: solvent surface code Date: Wed, 29 Mar 95 11:04:22 -0800 From: Richard Macdonald >>Does anyone have a program that will generate a >>set of equally spaced points (in xyz coordinates) >>on a surface of over-lapping spheres? I was impressed with the optimal distribution of points on the surface of a sphere given by Scott leGrand and Ken Merz in J Comp. Chem. 14, 349-352 (1993) in their paper titled, "Rapid Approximation to molecular surface area via the use of boolean logic and look-up tables". Their implementation minimizes the function: U(x,y) = SUM((180 - B)**2) where B is the arc length on the sphere in degrees between points x and y. -----> richard *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Lead Scientist fax: (619) 458-0136 Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 *********************************************************** From terence@mdli.com Wed Mar 29 14:12:48 1995 Received: from iat.holonet.net for terence@mdli.com by www.ccl.net (8.6.10/930601.1506) id NAA28656; Wed, 29 Mar 1995 13:57:39 -0500 Received: from jubal.mdli.com by iat.holonet.net (terence@mdli.com) id KAA02292; Wed, 29 Mar 1995 10:57:38 -0800 Received: from turing.mdli.com by jubal.mdli.com (AIX 3.2/UCB 5.64/9393.1) id AA41319; Wed, 29 Mar 1995 10:55:33 -0800 Received: by turing.mdli.com (931110.SGI/930416.SGI.AUTO) for @jubal.mdli.com:dough@mdli.com id AA29729; Wed, 29 Mar 95 09:38:15 -0800 From: "Terence Wilson" Message-Id: <9503290938.ZM29727@turing.mdli.com> Date: Wed, 29 Mar 1995 09:38:11 -0800 In-Reply-To: "Osman F. =?ISO-8859-1?Q?G=FCner?=" "fyi - if you would like to help this soul..." (Mar 29, 7:50am) References: <01HOP8J6L894QO6IKJ@mdli.com> X-Face: &`GoyLT!Ws86~k>+`:E>[)jlTu1-nr5s&X`R,['>ubs-'Y}iS$:gVA6wlrSY@#p)Dqp*[4M ^T^S40OCrD]Y!4vT8)./,;IM5bmLA_ X-Face-Info: MDL logo X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Osman F. =?ISO-8859-1?Q?G=FCner?=" Subject: Re: fyi - if you would like to help this soul... Cc: CHEMISTRY@ccl.net, dough@gimli.mdli.com, terence@turing.mdli.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Mar 29, 7:50am, Osman F. =?ISO-8859-1?Q?G=FCner?= wrote: > Subject: fyi - if you would like to help this soul... > From: IN%"S.R.Kilvington@soton.ac.uk" "Simon Kilvington" 29-MAR-1995 07:01:58.71 > To: IN%"CHEMISTRY@ccl.net" > CC: > Subj: CCL:Ring perception algorithms > > Dear all, > > does anyone have any references to ring perception algorithms? > All I need to know is whether each bond in a molecule is either cyclic > or acyclic. It's fairly easy to think of ways of doing it but I was > wondering if there are any cunning tricks that have been developed that > make it faster/use less memory etc. > > thanks for any help, > > Si. > > --- > Simon Kilvington, srk@soton.ac.uk >-- End of excerpt from Osman F. =?ISO-8859-1?Q?G=FCner?= Finding the cyclic/acyclic bonds in a graph can be done in polynomial time by walking the graph to deduce a spanning tree which can then be used to create a fundamental basis set of rings. Linear combinations of the basis set generate all possible rings in the graph. Downs et al. is the most comprehensive survey of ring perception algorithms: 'Review of Ring Perception Algorithms for Chemical Graphs'. Downs et al. JCICS 1989, 29, 172-187. -- "If you love your llama let it lambada." Terence Wilson terence@mdli.com tez@hooked.net 510 357 2222 x1300 MDL Information Systems 14600 Catalina St, San Leandro, Ca 94577, U.S.A. From lim@rani.chem.yale.edu Wed Mar 29 14:54:45 1995 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.10/930601.1506) id OAA29744; Wed, 29 Mar 1995 14:47:12 -0500 Received: by rani.chem.yale.edu; Wed, 29 Mar 95 14:47:12 -0500 From: Dongchul Lim Message-Id: <9503291947.AA06485@rani.chem.yale.edu> Subject: Re: solvent surface code To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 29 Mar 95 14:47:12 EST In-Reply-To: <9503291904.AA23877@iris26.biosym.com>; from "Richard Macdonald" at Mar 29, 95 11:04 am X-Mailer: ELM [version 2.3 PL11] > Does anyone have a program that will generate a > set of equally spaced points (in xyz coordinates) > on a surface of over-lapping spheres? > The following article proposes an improved 'marching-cube' method for molecular surface triangulation. -Dongchul Lim, Dept. of Chemistry, Yale Univ. X. Zhexin, S. Yunyu, and X. Yingwu, "Calculating the Electric Potential of Macromolecules: A Simple Method for Molecular Surface Triangulation", J. Comp. Chem. 1995, 16, 512-6. From raman@bioc01.uthscsa.edu Wed Mar 29 19:09:46 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id SAA06361; Wed, 29 Mar 1995 18:56:18 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 29 Mar 1995 17:59:00 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA17353; Wed, 29 Mar 95 17:56:22 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9503292356.AA17353@bioc01.uthscsa.edu> Subject: Re: CCL:solvent surface code To: lim@rani.chem.yale.edu (Dongchul Lim) Date: Wed, 29 Mar 1995 17:56:21 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9503291947.AA06485@rani.chem.yale.edu> from "Dongchul Lim" at Mar 29, 95 02:47:12 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2051 > > The following article proposes an improved 'marching-cube' method > for molecular surface triangulation. > -Dongchul Lim, Dept. of Chemistry, Yale Univ. > > X. Zhexin, S. Yunyu, and X. Yingwu, "Calculating the Electric > Potential of Macromolecules: A Simple Method for Molecular > Surface Triangulation", J. Comp. Chem. 1995, 16, 512-6. I belive that the marching cubes algorithm is already implemented in the program GRASP available from Anthony Nicholls (Barry Honig's group). He can be reached at nicholls@cuhhca.hhmi.columbia.EDU. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From monge@anny.psgvb.com Wed Mar 29 19:24:48 1995 Received: from anny.psgvb.com for monge@anny.psgvb.com by www.ccl.net (8.6.10/930601.1506) id TAA06722; Wed, 29 Mar 1995 19:11:03 -0500 Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA05479; Wed, 29 Mar 95 16:10:59 -0800 Date: Wed, 29 Mar 95 16:10:59 -0800 From: monge@anny.psgvb.com (Alessandro Monge) Message-Id: <9503300010.AA05479@anny.psgvb.com> To: chemistry@ccl.net Subject: Re: Molecular Modeling Packages for ALPHA systems Karl F. Moschner wrote: >Surprisingly DEC doesn't seem to be pursuing the computational chemistry >market as vigorously as it had in the VAX and DECsystem days. Still, there >are a slew of QCPE programs which have been ported to the DEC Alphas. Also: An addition to the list of computational chemistry packages that run on DEC Alpha workstations is Schrodinger's program PS-GVB: > DEC Alpha Software Supplier Contact > --------------------------------------------------------------------------- PS-GVB v2.1 Schrodinger, Inc. info@psgvb.com > --------------------------------------------------------------------------- The DEC version of PS-GVB includes an X/OpenGL based Graphical User Interface. PS-GVB is an ab initio quantum chemistry code which uses novel numerical technology (based on Pseudo-Spectral methods, originally developed for hydrodynamic simulations of turbolence) involving both basis sets and numerical grids. These algorithms yield substantial performance improvements for a wide variety of ab initio electronic structure methods as compared to any existing commercial quantum chemistry program. PS-GVB supports the following functionalities: * Hartree-Fock, Generalized Valence Bond (GVB), DFT, MP2, Local MP2, and GVB-RCI energies * accurate solvation energies, using a continuum solvent model based on the Poisson-Boltzmann equation and a realistic representation of the molecular cavity * optimization of molecular structures using HF, GVB, or DFT wavefunctions * frequencies for HF, GVB, or DFT wavefunctions, in gas phase or in solution * large variety of basis sets, including Pople, Dunning and Hay-Wadt ECPs * polarizabilities and hyperpolarizabilities * electrostatic potential charge fitting * multipole moments, from dipole through hexadecapole For more information on PS-GVB contact me by phone at (800) 20-PSGVB or e-mail to monge@psgvb.com. Alessandro ------------------------------------------------------------------------ Alessandro Monge Schrodinger, Inc. monge@psgvb.com (800) 20-PSGVB