From unipune.ernet.in!gadre@iucaa.ernet.in Mon Sep 23 02:30:50 1996 Received: from sangam.ncst.ernet.in for unipune.ernet.in!gadre@iucaa.ernet.in by www.ccl.net (8.7.5/950822.1) id BAA11724; Mon, 23 Sep 1996 01:52:27 -0400 (EDT) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id LAA00734 for CHEMISTRY@www.ccl.net; Mon, 23 Sep 1996 11:26:07 +0530 (GMT+05:30) >Received: from unipune.ernet.in by iucaa (4.1/SMI-4.1) id AA23818; Mon, 23 Sep 96 09:52:35+050 Received: from iucaa by sangam.ncst.ernet.in; Mon, 23 Sep 1996 11:26 GMT Received: from unipune.ernet.in by iucaa (4.1/SMI-4.1) id AA23818; Mon, 23 Sep 96 09:52:35+050 Received: by unipune.ernet.in (5.0/SMI-SVR4.1.0) id AA00807; Mon, 23 Sep 1996 09:34:55 +0500 Date: Mon, 23 Sep 1996 09:34:55 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9609231434.AA00807@unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: e-mail nos Content-Type: text Status: R Dear Sirs : Kindly send me the FAX and e-mail nos of the editorial offices of J. Phys. Chem., J. Chem. Phys. and J. Org. Chem. Thanks..................................Shridhar Gadre From sophie@ms532u02.u-3mrs.fr Mon Sep 23 09:30:56 1996 Received: from ms532u02.u-3mrs.fr for sophie@ms532u02.u-3mrs.fr by www.ccl.net (8.7.5/950822.1) id IAA15344; Mon, 23 Sep 1996 08:59:16 -0400 (EDT) From: Received: by ms532u02.u-3mrs.fr (AIX 3.2/UCB 5.64/4.03) id AA18351; Mon, 23 Sep 1996 15:00:08 +0100 Message-Id: <9609231400.AA18351@ms532u02.u-3mrs.fr> Subject: SUMMARY:Volume Comp. To: chemistry@www.ccl.net Date: Mon, 23 Sep 1996 15:00:08 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23alpha2] Content-Type: text I reported the summary of a question I posted two months ago. It was about the available programs to compute the vdw volume and/or solvent accessible volume. I removed the answers concerning commercial software such as Quanta, Spartan, Hyperchem, InsightII and Cerius2 Thanks for all the answers. C********************** From John (Usually chem8@york.ac.uk) SUBROUTINE MOLVOL c volume.f - volume determination code c c Author: Lawrence R. Dodd c Doros N. Theodorou c Doros N. Theodorou c Maintainer: Lawrence R. Dodd c Created: March 21, 1990 c Version: 2.0 c Date: 1994/07/22 15:45:51 c Keywords: volume and area determination c Time-stamp: <94/07/22 11:02:23 dodd> c Copyright (c) 1990, 1991, 1992, 1993, 1994 c by Lawrence R. Dodd and Doros N. Theodorou. C---------------------------------------------------------------------C C Plane Sphere Intersections C C---------------------------------------------------------------------C C This program will find the total and individual volume and C C exposed surface area of an arbitrary collection of spheres of C C arbitrary radii cut by an arbitrary collection of planes C C analytically by analyzing the plane/sphere intersections. C C---------------------------------------------------------------------C C Algorithm by: Doros N. Theodorou and Lawrence R. Dodd C C Coded by: L.R. Dodd C C---------------------------------------------------------------------C C Created on: March 21, 1990 C C Phase 1 Completed on: March 23, 1990 C C Phase 2 Completed on: April 16, 1990 C C Phase 3 Completed on: May 17, 1990 C C Phase 4 Completed on: June 5, 1990 C C Phase 5 Completed on: July 26, 1990 C C---------------------------------------------------------------------C C Reference: C C C C "Analytical treatment of the volume and surface area of C C molecules formed by an arbitrary collection of unequal C C spheres intersected by planes" C C C C L.R. Dodd and D.N. Theodorou C C MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991 C C---------------------------------------------------------------------C C Acknowlegement: C C C C LRD wishes to thank his mentor DNT for a stimulating and C C enjoyable post-doctoral experience. C C---------------------------------------------------------------------C C General Notes On Program: C C C C This program has been written with an eye towards both C C efficiency and clarity. On a philosophical note, many believe C C that these ideals are mutually exclusive but in general they C C are not. There are, however, a few instances where one ideal C C has been given more prominence over the other. The comments in C C the program, together with the associated journal article, C C should help to explain any apparent logical leaps in the C C algorithm. C C C C The program was intended to be used as a subroutine called C C repeatly by some main program. In this case the subroutine C C "VOLUME" is called by some main routine which has placed the C C necessary information in common block /Raw Data/. The answers C C are returned in common block /Volume Output/. I must apologize C C for the poor input/output for the program. For example, the C C area/volume of each sphere is not placed in /Volume Output/. C C C C This program was developed on a Sun SPARCstation 330 using Sun C C FORTRAN 1.3.1 (all trademarks of Sun Microsystems, Inc.). We C C have used some of extensions to the ANSI standard including: C C C C o long variable names (i.e., more than six characters) C C o variable names containing the characters '$' and '_' C C o END DO used in place of the CONTINUE statement C C o DO-WHILE used in place of IF-GOTO constructs C C o excessive number of continuation lines in some FORMATs C C o generic intrinsic function calls (e.g., SIN for DSIN) C C o IMPLICIT NONE statement (needed in development) C C C C The advantage of using non-standard FORTRAN is that it makes it C C considerably easier to follow the flow of a program. There are C C no extraneous statement labels in this program that may have C C obscured the logic (not a single GOTO was used). The previews C C of the new F90 standard appear to adopt many of the features C C already implemented in VMS, Sun, Cray, and IBM FORTRAN. C C C C Note that this algorithm is completely parallelizable. C C C C Larry Dodd C C dodd@mycenae.cchem.berkeley.edu C C C C Department of Chemical Engineering C C College of Chemistry C C University of California at Berkeley C C Berkeley, California 94720-9989 C C (415) 643-7691 (LRD) C C (415) 643-8523 (DNT) C C (415) 642-5927 (Lab) C C C C dodd@mycenae.cchem.berkeley.edu C C doros@mycenae.cchem.berkeley.edu C C C C---------------------------------------------------------------------C C Note: C C Plane_Ordering of common block /Debug/ is, as the name C C implies, for debugging purposes only as is routine ORDERING. C C The information contain therein is not necessary for solving C C the sphere plane problem but proved incredibly useful during C C program development. C C---------------------------------------------------------------------C C*********************** From: rolf@immunologie.charite.hu-berlin.de (Dr Rolf-Dietrich Stigler) Dear Philippe there is a program called msb from Connolly which does the job. For details, see Connolly, M.L. Solvent-Accessible Surfaces of Proteins and Nucleic Acids. Science 221(4612):709-713, 1983. For all I know, this program is also available via QCPE. Hope this helps. Rolf-Dietrich Stigler C*********************** From: "Magan Govender" .. Hi.. I have a program called surf...it is free and easy to use.. email if u require a copy... email : govendem@che.und.ac.za govendem@lourie.und.ac.za govendem@hoopoe.und.ac.za C*********************** From: D.E.Clark@proteus.co.uk (Dr David E. Clark) Dear Dr Camelio Try contacting: dodd@roebling.poly.edu (Larry Dodd) He once kindly supplied me with his Fortran code for molecular volume and surface area calculations. See also the reference: author = "Dodd, L.R. and Theodorou, D.N. ", title = "Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes ", journal = "Molecular Physics ", year = "1991 ", volume = "72 ", pages = "1313-1345 ", C*********************** From: waller@tyr.herl.epa.gov (Dr. Chris L. Waller) MS program, QCPE 429, claculates the coordinates of points on the solvent acessible surface of molecules. C*********************** From: MARTIN@cmdb.pprd.abbott.com SAVOL2 from Robert Pearlman, University of Texas is the best! Really fast and very flexible. Philippe Camelio Laboratoire de Stereochimie Marseille, France From qojskd@uscmail.usc.es Mon Sep 23 10:30:58 1996 Received: from uscmail.usc.es for qojskd@uscmail.usc.es by www.ccl.net (8.7.5/950822.1) id KAA15899; Mon, 23 Sep 1996 10:22:57 -0400 (EDT) Received: from [193.144.74.36] (qolera.usc.es) by uscmail.usc.es (5.67b/1.34) id AA07439; Mon, 23 Sep 1996 16:26:26 +0200 Date: Mon, 23 Sep 1996 16:26:26 +0200 Message-Id: <199609231426.AA07439@uscmail.usc.es> From: "F. Javier Sardina" To: CHEMISTRY@www.ccl.net Subject: Freeware for NMR processing on PC's Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: POPmail 2.3b5 Dear netters: We are pleased to introduce MestRe-C 1.0 (Magnetic Resonance Companion) for WINDOWS95, our (freeware) program, for processing NMR data. MestRe-C processes and analyzes 1D FID's and spectra from Bruker and Varian instruments (it can also import NUTS files). It implements several filters and Fourier transforms, phase and baseline corrections, integrations, peak picking, etc. The program is now available from ftp://qobrue.usc.es/pub/nmr/MestRe-C and ftp://www.ccl.net/pub/chemistry/software/MS-WINDOWS95/MestRe-C Further information about the program can be found in our home page: http://qobrue.usc.es/jsgroup/MestRe-C/MestRe-C.html Please send your suggestions for improvements, comments and bug reports to: F. Javier Sardina Departamento de Quimica Organica Universidad de Santiago de Compostela 15706 Santiago de Compostela SPAIN e-mail: qojskd@usc.es We are currently working on a version capable of processing 2D spectra and import data from other instruments. Any help with this task will be greatly appreciated. Happy NMR data processing F. Javier Sardina, J. Carlos Cobas and Jacobo Cruces F. Javier Sardina Phone: 34-81-563100. Ext. 14234 Departamento de Quimica Organica Phone: 34-81-591085 Universidad de Santiago de Compostela Fax: 34-81-595012 15706 Santiago de Compostela E-mail: qojskd@usc.es SPAIN http://qobrue.usc.es/jsgroup/js-eng.html