From tamasgunda@tigris.klte.hu Mon Aug 21 05:19:52 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950810.1506) id FAA17930; Mon, 21 Aug 1995 05:10:08 -0400 Message-Id: <199508210910.FAA17930@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Mon, 21 Aug 1995 11:10:25 EDT Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Mon, 21 Aug 1995 11:10:28 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Principal components summary Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Dear Netters, Some time ago I had a question about principal components and plane fitting to points. My original question was: I am looking for algorithm/numerical methods for the determining of the principal components of a data set. In the words of geometry, I have a number of points determined by y1, y2 and y3, and I am looking for the best fitting plane to the points, i.e. the plane determined by the two greatest principal components. Thanks for everybody who send me the answers. Here is the summary Tamas E. Gunda ------------------------------------------------------------ *************************************************** That looks like a rather straightforward least-squares problem. You want the parameters a,b,c in the equation for a plane y3 = a y1 + b y2 + c. So you make up a matrix X: y1(1) y2(1) 1 y1(2) y2(2) 1 ... y1(n) y2(n) 1 and a vector Z = (y3(1), y3(2), ..., y3(n)), plus a 3-component vector of unknowns A = (a,b,c). Then A = X^+ Z gives you the best values for the parameters, where X^+ is the generalized inverse of X. Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ********************************************* There are listings for FORTRAN programs pertaining to all aspects of factor analyses, including pca in "Factor Analysis of Data Matrices", P. Horst, Holt, Rinehart and Winston, New York, 1965. I also have written my own code, using the routines TRED2 and TQLI from "Numerical Recipes in Fortran" to diagonalize the covariance matrix and locate the eigenvalues and eigenvectors. Heather Gordon Department of Chemistry Queen's University Kingston, Ontario ******************************************** What you say you want sounds a lot like the transformation of a molecule to the coordinate system in which the moment-of-inertia tensor is diagonal. If your (y1, y2, y3) components are *orthogonal*, you ought to be able a similar approach. This kind of code is buried in all sorts of programs . It should be a simple matter to adapt a suitable code fragment to you use. FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com ******************************************** Tamas, A friend sent me your e-mail on the subject of an algorithm for calculating the first two PC's from a dataset. I have written PCA (NIPALS) routines in BASIC and C and will be happy to send them to you, if required. I also have a book (Numerical Recipes) which details PCA (Singular Value Decomposition) which does a similar thing. If you still need some help, send me an e-mail Steve Gurden, Bristol Chemometrics Group, School of Chemistry, University of Bristol, Cantock's Close, BRISTOL BS8 1TS Tel: +44 (0)117 9289000 extn. 4421 e-mail: S.P.Gurden@bris.ac.uk ******************************************** Dear Dr. Gunda, One of the most simple and elegant method to perform Principal Component Analysis is that of the NIPALS algorithm. It can be formulated in a few lines of programming and it works really fine. You can find it in the following references: * Analytica Chimica Acta, vol. 185, p. 1-17 (1986) * Chemometrics and Intelligent Laboratory Systems, vol. 2, p. 37-52 (1987) I hope this helps you. Sincerely. Jose I. Garcia -- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-350475 Departamento de Quimica Organica Fax : 34-(9)76-567920 Instituto de Ciencia de Materiales de Aragon e-mail: jig@qorg.unizar.es C.S.I.C.-Universidad de Zaragoza jig@msf.unizar.es E-50009 ZARAGOZA (SPAIN) ***************************************************** I thought the principle (no pun intended) was quite simple; just calculate the variance/covariance matrix of the variables (or better the correlation matrix) and diagonalize that. You can get the correlation matrix by autoscaling the data and calculating the covariance matrix then. Next, select the number of principal components that you want by calculating the cumulative sum of the eigenvalues divided by the sum of all the eigenvaeigenvectors need to be sorted by their size by the diagonalization procedure or afterwards) I mean: T = \sum_i \labda_i suppose, as an example: \labda_1 / T = 90 % (\labda_1 + \labda_2) / T = 98 % ... (\labda_1 + \labda_2 + ...) /T = .. if this is sufficiently accurate for you, use the subspace spanned by the first two eigenvectors as your new space, and project all datapoints onto it. otherwise, use more eigenvectors until (\sum_j \labda_j) / T is sufficiently near 100 % (1.00), and project the datapoints on the subspace (unfortunately it is no longer a 2-D plane, which would be most easy for viewing) Hopefully you can use this information, I can't think of any references off-hand.. There is a book by Box (and Hunter?) which describes these multivariate techniques in great detail. Sorry I can't help you better, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-274505 ******************************************** Check the NIST CD for handwritten characters -- there is a principal component algorithm coded there (may be in C, but you could then recode it in FORTRAN). There are several sites that catalog algorithms, too -- here are a few: http://gams.nist.gov/, http://netlib.att.com/netlib/att/cs/home/1127.ht, http://www.netlib.org/. Good luck. Joe McDaniel joe@psiint.com ******************************************** Dear Dr. Gunda, There are many references to Principal Component Analysis.It is actually a straightforward problem in matrix diagonalization. However, if your real goal is to simply fit a plane to a set of points (minimizing the sum of squares of the distances of the points to the plane) or a line to a set of points (minimizing the sum of squares of the distances of the points to the line), then this is also a simple matrix diagonalization problem whose solution is given and discussed in the following references: "To Fit a Plane or Line to a Set of Points by Least Squares", V. Schomaker, J. Waser, R.E. Marsh, and G. Bergman, Acta Cryst., vol. 12, pp. 600-604 (1959). and "To fit a plane to a set of points by least squares", D.M. Blow, Acta Cryst., vol. 13, p. 168 (1960). Regards, Marvin Waldman, Ph.D. Director, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com ******************************************** Dear Dr. Gunda, There are two ways to do what you want (as I understand it). One is to use a statistical analysis package which supports principal components analysis as statisticians define it. The plane you are looking for is the one defined by the first two principal components. The other is to perform the equivalent of a moment of inertia calculation with all masses set to 1. First find the mean value of each of the three coordinates (call them x, y, z). This is equivlant to your center of mass. Build the symmetric 3x3 tensor with the following elements, summed over all points (distances are relative to the centroid): y*y + z*z -x*y -x*z -x*y x*x + z*z -y*z -x*z -y*z x*x + y*y Diagonalize the tensor (the Jacobi method works well here - see any of the "Numerical Recipes" series by Press et all.) The transformation matrix gives you your three principal coordinates. Hope this helps, Paul Soper Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-8412 ******************************************** According to the math of the normal least square procedure, as far as I know, NOT the distances of the points and the line are minimized (i.e. a perdendicular from a point to the line), but the difference of the measured and the calculated y values,which is represented graphically by a line between the point and the regression line and it is parallel with the y axis: That depends on the error criterion that you use. The one sent yesterday (and probably some others too) does indeed minimize the error along one coordinate axis (and in fact works only if that axis does not lie in the plane that you want to fit). If you want to minimize the distances of the points from the plane, use the normal form for the plane: n x - d = 0, where n is the normalized normal vector, x is the coordinate vector, and d the distance of the origin from the plane. The distance of any point y from this plane is simply given by n y - d, so you must minimize __ \ | | 2 / | n y_i - d | -- i with the constraint that n is normalized, so you need a least-squaresminimizer that can handle constraints (e.g. via Lagrange multipliers). Or use a "dirty hack": if you know (or assume) that d will never be zero (i.e. the plane will not contain the coordinate origin), set d = 1 and use an unnormalized normal vector, whose length then is the inverse of the distance from the origin. Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ******************************************** What you say you want sounds a lot like the transformation of a molecule to the coordinate system in which the moment-of-inertia tensor is diagonal. If your (y1, y2, y3) components are *orthogonal*, you ought to be able a similar approach. This kind of code is buried in all sorts of programs. It should be a simple matter to adapt a suitable code fragment to you use. FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com ******************************************** Tamas, I think I have solved a problem fairly similar to the one you are interested in. My problem was less general and involved finding thebest-fit plane to a group of four points centred around a fifth point and arose because I am looking at compression strain in tetracoordinate carbon systems. For example the molecule [4.4.4.4]fenestrane C9H12 H H2C__C__CH2 | | | HC-----CH | | | H2C--C--CH2 H contains a central "flattened" tetracoordinate carbon atom. One way to determine the flattening at any C(C)4 moiety is to find the best-fit plane for the four alpha-C atoms passing through the central C atom. This can be done simply by finding the eigenvectors of what we have termed the Geometry Tensor. The Geometry Tensor is constructed by multiplying the matrix D (the vectors to your points -- in this case the 4 alpha-C atoms) by its transpose to give a 3x3 Real Symmetric Matrix (routines to find the eigenvectors/values of any RSM can be found in eispak and similar sets of routines). The eigenvectors of this matrix will correspond to the minimum (Best-Fit) -- this will have the smallest eigenvalue, maximum and one other extremum (i.e. they will form a set of cartesian axes -- x,y and z -- one of which will be the normal to your best-fit plane. The mathematics behind this is actually quite simple and involes setting up the equations to minimise d' = (sum of squared distances of your points to an orbitrary plane). After which the need to form and find the eigenvectors of the "Geometry Tensor" becomes obvious. Naturally this can be readily extended to any number of atoms and any origin. I have used this method to re-orient molecules that were optimised in C1 symmetry (in cartesians) which exhibit higher symmetry but where the axes/planes of symmetry do not lie on the x,y or z axes of my final cartesians. I might be able to send you my fortran code (it is very simple) if you think this would help but I will need to check the origin of the eigenvector solving routines that I use (to make sure we do not break anyone's intellectual property rights as I did not write these routines myself -- I think they came from eispak). Cheers, Danne Danne R Rasmussen, PhD Student phone: +61 6 249-3771 Research School of Chemistry fax: +61 6 249-0750 Australian National University Canberra ACT 0200 e-mail: danne@rsc.anu.edu.au ******************************************** Hi, Your assumption about the fitting of the least squares of perpendicular distances is correct .. this is what is done by linear regression. A side note, linear regression is used in teaching software, but programs are always built around the matrix formulation. The way that you can fit perpendicular distances, as well as do non-linear fits (constants other than linear coeficients) is using optimization methods, such as steepest descent, Newton-Rhapson, etc. This is just like doing geometry optimization, only you are minimizing on your perpendicular distances instead of energy. The other possibility is spline methods (cube splines are most commonly used). A spline method is not a least square fit, it is an exact fit. However, if there is noise in the data you fit exactly to the noise. Hope this helps. Dave Young young@slater.cem.msu.edu ******************************************** From: g80@chm.uri.edu Hi Dr. Tamas Gunda, I too have been interested in the question of fitting a plane to a set of points(3D). As you correctly pointed out this is a problem in total least squares, not simple least squares. This problem as been approached many times using a variety of algorithims(its' fundamental to crystallography). I have written a simple FORTRAN program based on the method of D. M. Blow, Acta. Cryst.(1960),13,168. One fundamental paper is V. Schomaker, J. Waser, R. E. Marsh and ?. Bergman, Acta Cryst(1959),12,60. There are many other papers on this subject. I hope this helps and good luck. Brian Schmitz Univ. of Rhode Island *************************************************** summary end here ***************************************************************************** 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 ferenc@rchsg8.chemie.uni-regensburg.de Mon Aug 21 05:34:50 1995 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.10/950810.1506) id FAA17984; Mon, 21 Aug 1995 05:21:10 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA09657 (5.65c/IDA-1.4.4 for ); Mon, 21 Aug 1995 11:20:43 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA12238; Mon, 21 Aug 95 11:19:02 +0200 Date: Mon, 21 Aug 95 11:19:02 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9508210919.AA12238@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: water and argon Dear Netters: I am trying to run MD calculations for a system consisting of argon atoms and water molecules. Can anybody provide me with some LJ12-6 nonbonding parameters for this system. Every pointer is very wellcome. I did a literature search, but the parameters I found were not very successfull in reproducing some of the experimental facts. Thank you very much in advance! Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) ...THE PHYSICISTS HAVE MADE THEIR UNIVERSE, AND IF YOU DO NOT LIKE IT, YOU MUST MAKE YOUR OWN. -- E. R. HARRISON IN "COSMOLOGY" (1980) --------------------------------------------------------------------------- From Jeffrey.Gosper@brunel.ac.uk Mon Aug 21 05:49:51 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950810.1506) id FAA18047; Mon, 21 Aug 1995 05:35:20 -0400 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <13414-0@monge.brunel.ac.uk>; Mon, 21 Aug 1995 10:34:34 +0100 Date: Mon, 21 Aug 1995 10:34:34 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:normal modes visualisation To: Godbout Nathalie cc: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Thu, 17 Aug 1995 13:00:36 -0400 (EDT) Godbout Nathalie wrote: > From: Godbout Nathalie > Date: Thu, 17 Aug 1995 13:00:36 -0400 (EDT) > Subject: CCL:normal modes visualisation > To: CHEMISTRY@www.ccl.net > > > Hello CCL members, > > I am in need of a program that will help me visualize > the nature of the calculated normal modes of molecules. > Specifically, the commonly found illustrations of arrows > along bonds would be helpful. The molecules contain > between 20-25 atoms, hence the difficulty in interpreting > the results of the vibrational analysis. > > Many thanks in advance for your help. > > Nathalie If the results come from a MOPAC calculation then my program Re_View to be published shortly by the ACS can animate them. Re_View runs under Windows. Contact at the ACS is Julie Bargo /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ 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://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From hebant@ext.jussieu.fr Mon Aug 21 07:34:51 1995 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.6.10/950810.1506) id HAA19095; Mon, 21 Aug 1995 07:24:21 -0400 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id NAA14883 for ; Mon, 21 Aug 1995 13:24:13 +0200 Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Mon, 21 Aug 1995 13:24:01 +0200 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Aug 1995 13:26:57 +0100 To: CHEMISTRY@www.ccl.net From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: Pseudopotentials Can someone tell me what is exactly a pseudopotential and what is the difference between a potential and a pseudopotential. ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 e-mail hebant@ext.jussieu.fr Visitez notre serveur WWW : http://alcyone.enscp.jussieu.fr/ From PHYSPLMP@MIZZOU1.missouri.edu Mon Aug 21 10:49:55 1995 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.10/950810.1506) id KAA21520; Mon, 21 Aug 1995 10:48:50 -0400 From: Message-Id: <199508211448.KAA21520@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R3) with BSMTP id 6827; Mon, 21 Aug 95 09:50:03 CDT Received: by MIZZOU1 (Mailer R2.10 ptf000) id 0266; Mon, 21 Aug 95 09:50:02 CDT Date: Mon, 21 Aug 95 09:48:41 CDT To: landin@membrana.mednet.gu.se cc: chemistry@www.ccl.net, landin@clavicula.mednet.gu.se, dave@wh.bayer.com Subject: Re: CCL:RE PM3 for phosphates In-Reply-To: landin@membrana.mednet.gu.se -- Sat, 19 Aug 1995 00:11:08 -0600 I'd appreciate receiving a reprint. Pat Plummer, Univ. of Missouri, Columbia MO 65211 (Dept of Physics) PHYSPLMP@mizzou1.missouri.edu From jkl@ccl.net Mon Aug 21 11:34:56 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id LAA22213; Mon, 21 Aug 1995 11:30:45 -0400 Received: from UTARLG.UTA.EDU for B314U09@utarlg.uta.edu by bedrock.ccl.net (8.6.10/930601.1506) id LAA03811; Mon, 21 Aug 1995 11:30:44 -0400 From: Received: from utarlg.uta.edu by utarlg.uta.edu (PMDF V4.3-10 #8453) id <01HUBYBCIBM8004Z60@utarlg.uta.edu>; Mon, 21 Aug 1995 10:30:42 -0500 (CDT) Date: Mon, 21 Aug 1995 10:28:58 -0500 (CDT) Subject: gamess To: chemistry@ccl.net Message-id: <01HUBYC3KG3M004Z60@utarlg.uta.edu> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, could anyone point me to a ftp or www site where I can find the latest version of GAMESS? Thanks in advance: Agnes Derecskei Dept. of Chemistry University of Texas at Arlington From jkl@ccl.net Mon Aug 21 11:36:05 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id LAA22220; Mon, 21 Aug 1995 11:30:56 -0400 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by bedrock.ccl.net (8.6.10/930601.1506) id LAA03815; Mon, 21 Aug 1995 11:30:46 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id VAA10657 for chemistry@ccl.net; Mon, 21 Aug 1995 21:01:08 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA19911; Mon, 21 Aug 95 20:57:53+050 Message-Id: <9508211557.AA19911@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Mon, 21 Aug 95 14:43:10 +0530 Date: Mon, 21 Aug 95 14:43:10 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:homology modeling package X-Vms-Mail-To: UUCP%"Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr" ==>I have recently heard about Modeler from MSI, have you still ==>used this software and do you have any comments ? ==>Thanks ==> ==>Dom ==> ==>Jean-Dominique Guitton ==>Rhone Poulenc Rorer Central Research ==>France ==>e-mail: jean-dominique.guitton@rp.fr If it is same modeller as supplied by Sali, then i must say it t sgood package. It works well and has a reasnoably good command language. Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From jkl@ccl.net Mon Aug 21 13:19:56 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id NAA23957; Mon, 21 Aug 1995 13:15:30 -0400 Received: from UTARLG.UTA.EDU for B314U09@utarlg.uta.edu by bedrock.ccl.net (8.6.10/930601.1506) id NAA05373; Mon, 21 Aug 1995 13:15:28 -0400 From: Received: from utarlg.uta.edu by utarlg.uta.edu (PMDF V4.3-10 #8453) id <01HUC1XFHXNK004XJS@utarlg.uta.edu>; Mon, 21 Aug 1995 12:15:26 -0500 (CDT) Date: Mon, 21 Aug 1995 12:13:42 -0500 (CDT) Subject: thanks for gamess info To: chemistry@ccl.net Message-id: <01HUC1YSBCFO004XJS@utarlg.uta.edu> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, thank you everyone who helped me to find the location of gamess and contact mike. Your help is very much appreciated. Agnes Derecskei Dept. of Chemistry University of Texas at Arlington From mrigank@imtech.ernet.in Mon Aug 21 15:04:58 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/950810.1506) id PAA26091; Mon, 21 Aug 1995 15:01:38 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id AAA02761 for chemistry@www.ccl.net; Tue, 22 Aug 1995 00:32:04 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA29575; Tue, 22 Aug 95 00:31:34+050 Message-Id: <9508211931.AA29575@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Mon, 21 Aug 95 21:18:30 +0530 Date: Mon, 21 Aug 95 21:18:30 +0530 From: Mrigank To: chemistry@www.ccl.net Subject: Cl Parametres: Summary. Some time back I posted a querry as follows: I am doing some simulations which includes a molecule containing Chlorine. Can any one suggest NB, angle and dihedral angle parametrs for it. For anlgels it is attached to a benzene ring substituting hydrogen. I would appreciate parameters that will go with AMBER 91 or OPLS force field. These are the responses : ________________________________________________________________________ From: Garcia Edgardo We are using the following vdW parameters in our simulations: Cl Re= 3.513 E=0.227, They are from UFF 1.01 corrected for OPLS functional form. __________________________________________________________________________ From: ross@cgl.ucsf.EDU You might want to look at the params we used for Br in nucleic acids in Effects of Nucleotide Bromination on the Stabilities of Z- RNA and Z-DNA: A Molecular Mechanics / Thermodynamic Perturbation Study. W. S. Ross, C. C. Hardin, I. Tinoco, Jr., S. N. Rao, D. A. Pearlman and P. A. Kollman. Biopolymers 28, 1939 (1989). for general comparative purposes.. the angle/bending/dihedral params were chosen by analogy w/ other params, so no special authority is implied. _________________________________________________________________________ From: edvard@atf1.fagmed.uit.no (Oyvind Edvardsen) For the NB parameters of Cl I used (some years ago) 1.95 A for the vdW radius and 0.2 kcal mol-1 for the well depth. The radius was extrapolated from the radii of S and P, and the well depth was the same as for S and P. These parameters were suggested by prof. P. A. Kollman. Angle and torsion parameters used, were equal to the generalized X-CA-X and X-CA-CA-X parameters in the AMBER 3.0 force field. Veenstra et al, J. Comput. Chem. 1992, 13(8), 971-78, used 2.25 A and 0.2 for CH3Cl NB params. ______________________________________________________________________________ From: Lipkowitz A list of published force field parameters exists as Appendix I in Reviews in Computational Chemistry, Volume 6, VCH Publishers, 1995. I don't recall if the Cl parameters you need are in there, but, it's a good source of information about parameters for various EFFs. Kenny _______________________________________________________________________________ Thanks to all. Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From BWLCM@jazz.ucc.uno.edu Mon Aug 21 20:20:01 1995 Received: from jazz.ucc.uno.edu for BWLCM@jazz.ucc.uno.edu by www.ccl.net (8.6.10/950810.1506) id UAA01699; Mon, 21 Aug 1995 20:05:54 -0400 From: Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01HUCGCIOGUO91Z7ZS@jazz.ucc.uno.edu>; Mon, 21 Aug 1995 19:05:07 CST Date: 21 Aug 1995 19:05:07 -0600 (CST) Subject: Searching for CHEMSITE To: chemistry@www.ccl.net Message-id: <01HUCGCIOGUQ91Z7ZS@jazz.ucc.uno.edu> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT ********************************************************************** Dear Colleagues, I am looking for a company selling a product called CHEMSITE. They market a windows-based drawing program. I would apreciate any information. Thank you Blaise LeBalanc, University of New Orleans bwlcm@jazz.ucc.uno.edu From jkl@ccl.net Mon Aug 21 21:50:03 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id VAA02388; Mon, 21 Aug 1995 21:42:46 -0400 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by bedrock.ccl.net (8.6.10/930601.1506) id VAA12752; Mon, 21 Aug 1995 21:42:41 -0400 From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA19937; Tue, 22 Aug 1995 09:42:05 +0900 Date: Tue, 22 Aug 1995 09:42:05 +0900 Message-Id: <9508220042.AA19937@chu.chem.nthu.edu.tw> To: chemistry@ccl.net, chpajt@bath.ac.uk Subject: Re: CCL:Wat15 sbound & charmm Dear Dr. Long, We still have problems to fix G94 PCM. Once we fix it we'll inform you a.s.a.p. Sincerely, Chu