From hutschka@quantix.u-strasbg.fr Wed Oct 2 04:13:32 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.7.5/950822.1) id DAA11676; Wed, 2 Oct 1996 03:30:28 -0400 (EDT) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA33151; Wed, 2 Oct 1996 09:31:18 +0200 Date: Wed, 2 Oct 1996 09:31:18 +0200 Message-Id: <9610020731.AA33151@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: SUMARY:PD atomic charges Cc: hutschka@quantix.u-strasbg.fr Hello, Last week I posted a question about the methods to get atomic charges. Here is my original question: I'm calculating atomic charges with Gaussian using Mulliken population analysis and fitting to electrostatic potential methods. I've noted some important differences between Mull and ESP derived charges. More , for ESP derived charges the use of correlated densities (MP2 density in this case) gives important differences with the use of HF density. So I would like to know if someone could advise me some references (review article would be nice) about the comparison of this methods and about the effect of correlation on the caculated charges. Another question : Does it make sense to do a Mulliken population analysis with the MP2 density ?? Any comment or help is welcome. Results will be summarized for everybody. Thanks. Here is the sumary of the answers I got: ******************************************** >From Dr. Donald E. Williams University of Louisville E-Mail: dew01@xray5.chem.louisville.edu ******************************************** New Software Available Molecular interactions occur during host-substrate docking, cluster, and crystal formation - whenever molecules associate with one another. The energy and geometry of molecular association is determined by the force field. As a component of the force field, an accurate set of net atomic charges is needed. Reliable net atomic charges can be found by fitting the molecular electric potential with program PDM96. The program provides a choice of geodesic, Connolly, cubic, or user specified grid points for the electric potential. In addition to net atomic charges, program PDM96 also allows any combination of atomic dipoles/quadrupoles, bond dipoles, as well as the addition of lone pair electron sites if required. A particularly useful feature of the program is the transparent way in which fixed charges and charge dependency conditions are specified. By specififying appropriate charge dependencies (e.g., equal charges or equal sums of charges), chemical intuition can assist to produce charges which are transferable between related types of molecules. A complete error treatment with standard deviations and correlations is made. Program PDM96, Potential Derived Multipoles The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM96 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on any computer with F77 capability. Program PDM96 has a unique combination of features: o excellent agreement with quantum mechanical multipole moments o general sites, e.g. united atoms, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 or G-94 output file o generalized input from other quantum mechanics programs o geodesic, Connolly, and cubic grids for MEP are available o provision for custom generation of MEP grid points o error analysis with standard deviations and correlations o on-line program manual o comprehensive examples are provided A review of potential-derived charges may be found in Reviews of Computational Chemistry, Vol. II, pp. 219-271 (1991). For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. Tel:(502)852-5975 Fax:(502)852-8149 E-mail:dew01@xray5.chem.louisville.edu ----------------------------------------------------------------------- Ordering information Program package consisting of manuals, Fortran-77 source files, and demonstration example files....................................$2,000 Special discount price is available for academic use only... ........$395 Normal shipment is via ftp; please provide an account protected with a temporary password to receive the program. Inquire about shipment via other media. Make check payable to the University of Louisville and mail to: Dr. Donald E. Williams Department of Chemistry University of Louisville Louisville, KY 40292 ------------------------------------------------------------------------- ************************************************ >From Bill Ross E-Mail: ross@cgl.ucsf.EDU ************************************************ We have references & discussion on http://www.amber.ucsf.edu/amber/ - see the section on the Cornell et al. force field and the one on charge derivation philosophy. Bill Ross ************************************************ >From Konrad Hinsen Laboratoire de Dynamique Moleculaire Institut de Biologie Structurale 38027 Grenoble Cedex 1, France E-Mail : hinsen@ibs.ibs.fr ************************************************ > I'm calculating atomic charges with Gaussian using Mulliken population > analysis and fitting to electrostatic potential methods. You didn't say *why* you are doing this, so I assume that the goal is obtaining partial charges for an empirical force field. > I've noted some important differences between Mull and ESP derived charges. > More , for ESP derived charges the use of correlated densities (MP2 density in this case) > gives important differences with the use of HF density. First of all, Mulliken charges are based on a somewhat arbitrary assignment of parts of electron densities to the individual atoms. They may give some indication of polarization etc., but as a source for partial charge information they are not very useful. ESP-derived charges depend on 1) the ab-initio reference potential (which includes basis-set dependence) 2) the choice of evaluation points for the potential 3) the method used for fitting the charges. Dependence 1) is obvious and if you find that your charges depend on the level of calculation (provided that you haven't done something stupid regarding 2) and 3)), then this is a feature of your system that you have to understand and draw conclusions from. The dependence on the evaluation points is equally obvious, but there is no single choice that everyone agrees on (and to some extent it depends on what you want to do with the fitted charges). Among the strategies that have been proposed are: 1) points on a grid around the molecule (not recommendable due to the dependence on arbitrary grid axes) 2) points on well-defined surfaces around the molecule 3) points chosen at random in a well-defined region around the molecule. Dependence 3) is more problematic, since it shouldn't be there in an ideal world. The proposed methods differ in numerical stability and in the exact quantity they are trying to minimize. Basically, everyone agrees that what we want is a least-squares fit. Such fits are in general known to be problematic, because the solution is often underdetermined, and this also occurs for charge fitting. It is therefore *not* a good idea to simply solve the normal equations for the least-squares, but unfortunately that is what most people are doing. A much safer alternative is singular-value decomposition, as described in most books on matrix computations, or even in the second edition of Numerical Recipes. Beyond the problem of numerical stability of the fit, one popular method (known as RESP) proposes to put a constraint on the absolute value of the charges, based on the observation that ESP often gives charges that seem to large. I don't know in how far this is a result of numerical instabilities (RESP does not use singular value decomposition) or of some real physical effect; this ought to be investigated. Literature: C.I. Bayly, P. Cieplak, W.D. Cornell and P.A. Kollman J. Phys. Chem. 97, 10269 (1993) (This paper describes RESP.) K. Hinsen and B. Roux J. Comp. Chem., in print (contact me for a preprint) (This paper describes a specific potential function for proton transfer simulations, but contains an extensive appendix that describes a charge-fitting strategy based on singular-value decomposition.) Both papers contain references to older methods. There is another paper that has appeared earlier this year in J. Comp. Chem. and which deals explicitly with an SVD-based fitting method, but I haven't seen it yet. The reference of this paper is: M. M. Francl, C. Carey, L. M. Chirlian, D. M. Gange, J. Comp. Chem, Vol 17, No 3, (1996), p 367-383 ******************************************************** >From Christopher J. Cramer University of Minnesota E-Mail : cramer@maroon.tc.umn.edu WWW : http://pollux.chem.umn.edu/~cramer ******************************************************** You might be interested in our extensive comparison of charges calculated by various methods (including our own CM1 methodology) in Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. " Class IV Charge Models: A New Semiempirical Approach in Quantum Chemistry" J. Comput.-Aid. Mol. Des. 1995, 9, 87. This paper is actually maintained on the Web by JCAMD. You can find it at http://wucmd.wustl.edu/jcamd/278/paper.html ******************************************************** >From Guosheng LI Lab. de Chimie Theorique Univ. de Nancy-I E-Mail : li@pink.incm.u-nancy.fr ******************************************************** For a good review, see S.M.Bachrach, "Population analysis and electron densities from quantum mechanics", in Reviews in Computational Chemistry, Vol.V K.B.Lipkowitz and D.B.Boyd, VCH publishers, Inc. New York, 1994, Chap.3 p.171-227. You may also refer to a recent paper: S.Tsuzuki et al., " Comparison of atomic charge distributions obtained >from different procedures: basis set and electron correlation effects" J. Mol. Struc.(Theochem), 365(1996),81-88. By the way, your interest is on "single-bonded" systems or "multiple-bonded" systems, and on isolated molecules or complex ? Electron correlation may have different effects on them. As for the former point, I agree with Bachrach's opinion, i.e. the effect of electron correlation on atomic populations is quite small for single- bonded systems, while much more substantial for multiple-bonded systems. For complex, situations are much more difficult and according to my experience, no one procedure can be satisfactory in most of the cases. (Hope this is not true !) Hope you will have some new findings. Guosheng LI Lab. de Chimie Theorique Univ. de Nancy-I li@pink.incm.u-nancy.fr *********************************************************************** I would like to thank everybody for the references and advices given. I hope this sumary will help everybody. Francois. ============================================================================= ¤ François HUTSCHKA Ph.D. Student in Quantum Chemistry ¤ ¤ ¤ ¤ Laboratoire de Chimie Quantique ¤ ¤ UPR 139 du CNRS ¤ ¤ 4, rue Blaise Pascal Phone: (33).88.41.60.32 ¤ ¤ 67000 STRASBOURG Fax: (33).88.61.20.85 ¤ ¤ FRANCE E-Mail: hutschka@quantix.u-strasbg.fr ¤ ============================================================================= From ccolo@mompou.iqs.url.es Wed Oct 2 05:56:36 1996 Received: from fletxa.iqs.url.es for ccolo@mompou.iqs.url.es by www.ccl.net (8.7.5/950822.1) id FAA12204; Wed, 2 Oct 1996 05:41:41 -0400 (EDT) Received: from mompou.iqs.url.es by fletxa.iqs.url.es (AIX 4.1/UCB 5.64/4.03) id AA34040; Wed, 2 Oct 1996 11:43:49 +0200 Date: Wed, 2 Oct 1996 11:33:28 +0100 (GDT) From: Carles Colominas To: chemistry@www.ccl.net Subject: deltaG of solvation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, our group is working on the calculation of free energies of solvation of a series of nitriles. Also we combine pairwise the deltaGs of solvation in different solvents to estimate log P values between those pairs of solvents... We need now experimental measures of deltaG of solvation of the studied systems (cyano compounds) as well as experimental logP values to compare the quality of our results. A good source of experimental data for water is a paper of Cabani (Cabani et al. Journal of Solution Chemistry, vol.10, No.8, p.563 (1981)). Since I cannot find some of our systems in the literature I would like to know other useful sources for ENERGIES of SOLVATION and logPs. Solvents of interest are water, chloroform, carbon tetrachloride instead of the widely used water/octanol pair with planty of available experimental data. Answers will be summarized. Thanks in advance, CC _______________________________________________________________________ Carles Colominas Dept. of Org. Chem. E-mail ccolo@mompou.iqs.url.es Institut Quimic de Sarria. TEL: (34-3)-203.89.00 Universitat Ramon Llull. FAX: (34-3)-205.62.66 Via Augusta 390. 08017-Barcelona. CATALONIA. _______________________________________________________________________ From berriz@chasma.harvard.edu Wed Oct 2 09:56:34 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.7.5/950822.1) id IAA01228; Wed, 2 Oct 1996 08:58:40 -0400 (EDT) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA24123; Wed, 2 Oct 1996 08:58:41 -0400 Date: Wed, 2 Oct 1996 08:58:41 -0400 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9610021258.AA24123@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: Sample parallelized MD code wanted I am taking my first steps into parallel programming (though I'm an experienced [serial] C programmer). I'm looking for sample code to use as a learning aid. The ultimate application I have in mind is a simplified MD-type algorithm, therefore parallelized MD code would be ideal. Also, I'd very much welcome any pointers to useful resources for parallel programming novices. Thanks in advance for your suggestions. Gabriel Berriz berriz@chasma.harvard.edu From jose@zeus.uncor.edu Wed Oct 2 10:56:36 1996 Received: from zeus.uncor.edu for jose@zeus.uncor.edu by www.ccl.net (8.7.5/950822.1) id KAA02077; Wed, 2 Oct 1996 10:35:15 -0400 (EDT) Received: by zeus.uncor.edu; id AA23984; Wed, 2 Oct 1996 11:41:41 -0300 Sender: jose@zeus.uncor.edu Message-Id: <32527F24.41C6@zeus.uncor.edu> Date: Wed, 02 Oct 1996 11:41:40 -0300 From: "Jose Santiago Duca (h)" Organization: INFIQC - Dpto Qca Organica - Facultad de Ciencias Quimicas - Universidad Nacional de Cordoba X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Cc: jose@zeus.uncor.edu Subject: Bug in G94?? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, If you are a G94 user, you will find the next bug in Lnk1e when running ----------------------------- # b3lyp/lanl2dz freq=NoRaman h2 0 1 h h 1 0.95 ----------------------------- the log file is .... # ub3lyp/lanl2dz freq=NoRaman ----------------------------- No analytic 2nd derivatives for this method. Error termination via Lnk1e in /usr/theory/g94/g94/l1.exe. ----------------------------- However, G94 do calculate analytic 2nd derivatives for the ub3lyp method, as it is demonstrated when you submit the following input ----------------------------- # ub3lyp/lanl2dz freq h2 0 1 h h 1 0.95 ----------------------------- and the calculation ends succesfully. Conclusion: you cannot save this '20 %' of the total time usually spent in the Raman calculation... and it's a pity cheers Jose p.s. any comments are welcome, bye. -- Dr. Jose Santiago Duca (h) jose@zeus.uncor.edu http://zeus.uncor.edu/jsd/jsd.htm From shaomeng@helix.nih.gov Wed Oct 2 17:56:35 1996 Received: from helix.nih.gov for shaomeng@helix.nih.gov by www.ccl.net (8.7.5/950822.1) id RAA04346; Wed, 2 Oct 1996 17:15:24 -0400 (EDT) Received: (from shaomeng@localhost) by helix.nih.gov (950413.SGI.8.6.12/8.6.12) id RAA28787; Wed, 2 Oct 1996 17:15:17 -0400 Date: Wed, 2 Oct 1996 17:15:17 -0400 From: Shaomeng Wang Message-Id: <199610022115.RAA28787@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Motif software! Cc: shaomeng@helix.nih.gov Dear CCL friends, Could any provide me the information on the software/database for searching for known protein motifs? I appreciate very much your information. Shaomeng Wang, Ph.D. Georgetown University Medical Center From shaomeng@helix.nih.gov Wed Oct 2 18:06:38 1996 Received: from helix.nih.gov for shaomeng@helix.nih.gov by www.ccl.net (8.7.5/950822.1) id RAA04360; Wed, 2 Oct 1996 17:17:43 -0400 (EDT) Received: (from shaomeng@localhost) by helix.nih.gov (950413.SGI.8.6.12/8.6.12) id RAA29421; Wed, 2 Oct 1996 17:17:41 -0400 Date: Wed, 2 Oct 1996 17:17:41 -0400 From: Shaomeng Wang Message-Id: <199610022117.RAA29421@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Synthetic Chemistry List? Cc: shaomeng@helix.nih.gov Dear CCL friends, Does any know if there if a Synthetic Chemistry/Medicinal Chemistry List similar to the Computational Chemistry List? Thanks a lot for your information. Shaomeng Wang, Ph.D. Georgetown University Medical Center shaomeng@helix.nih.gov From dimitris@3dp.com Wed Sep 25 10:31:23 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.7.5/950822.1) id KAA09505; Wed, 25 Sep 1996 10:27:01 -0400 (EDT) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA27809; Wed, 25 Sep 96 10:33:00 -0400 Received: by europa.3dp.com (950413.SGI.8.6.12) id KAA13621; Wed, 25 Sep 1996 10:30:47 -0400 From: "Dimitris Agrafiotis" Message-Id: <9609251030.ZM13619@europa.3dp.com> Date: Wed, 25 Sep 1996 10:30:46 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Su: amino acid exchange matrices As promised, I attach a summary of responses to my posting regarding amino acid exchange matrices for protein sequence analysis. ______________________________________________________________________________ On Sep 17, 11:52am, Mark Johnson MOL wrote: > > Matrices, we have. I enclose our file from our www pages, > about a dozen or so matrices, references our comparison papers. > See Johnson & Overington 1993 JMB where we compared these matrices; > Se all Vogt et al (1995) JMB 249, 816 > where they consider an even larger group of matrices. > > Good luck, Mark Johnson > > from html page ... > > Matrices for comparing sequences obtained from different published works. > Includes Dayhoff 250 & 120 PAM matrices, Gonnet, Henikoff & Henikoff, > Johnson & Overington 1993, Rao, and others. > > /* > * MAY BE FREELY DISTRIBUTED WITH THE PERMISSION OF THE AUTHOR > * > * As with most things in life, use is at your own risk (except > * in the States where accidents and misfortunes are not permitted > * under the lawyers' Bill of Free Enterprise). > * > * Mark S. Johnson, Modelling and Biocomputing Group, Center > * for Biotechnology, PO Box 123, FIN-20521 TURKU, FINLAND > * FAX: 358-21-633-8000 Email: mark@hops.btk.utu.fi > * > */ > > References: > > Johnson, M.S. & Overington, J.P. (1993). > "A structural basis for the comparison of sequences: An > evaluation of scoring methodologies." J. Mol. Biol. 233, 716-738. >

> Johnson, M.S., Overington, J.P. & Blundell, T.L. (1993). > "Alignment and Searching for Common Folds Using a Data Bank of Structural > Templates." > J. Mol. Biol., 231, 735-752. >

> Johnson, M.S., May, A.C.W., Rodionov, M.A. & Overington, J.P. (1996). "Discrimination of common protein folds: > applications of structural information to sequence/structure comparisons," > Methods in Enzymology 266, 575-598. >

> Johnson, M.S, Overington, J.P., Edwards, Y., May, A. & Rodionov, M.A. (1994). > "An integrated approach to the comparison of structures and sequences: > alignment, searching and the detection of common folds." > Proc. 27th Hawaii Intern. Conf. Syst. Sci. V, 296-305. >

> Overington, J.P., Donnelly D., Johnson, M.S., \(vSali A. & Blundell, T.L. > (1992). "Environmental specific amino acid substitution tables: > tertiary templates and prediction of protein folds." > Protein Science 1, 216-226. >

> Overington, J.P., Johnson, M.S., \(vSali, A. & Blundell, T.L. (1990). > "Tertiary constraints on protein evolutionary diversity: Templates, > key residues and structural prediction." > Proc. Roy. Soc. London B 241,132-145. >

> 
> /* mat.h		msjohnson		*/
>  *	different matrices (PAM250 etc) including one based on 110
>  *	aligned 3D structures: STRMAT110
>  *      computed according to:
>  *		Johnson & Overington (1993) J. Mol. Biol. 233:716-738
>  *      see Johnson, Overington & Blundell (1993) J. Mol. Biol. 231:735-752.
>  *          Overington, Johnson, Sali & Blundell (1990) Proc. Roy. Soc.
London
>  *	    ser. B, 241:146-152.
>  *	    Sali & Overington (1994) Prot. Sci. 3:1582-1596.
>  */
>
> /*
> ##
> ##  TRADITIONAL DISCLAIMER
> ##
> ##  Copyright 1988-1996 John Overington & Mark Johnson
> ##
> ##  Permission to use, copy, modify, and distribute this data, software
> ##  and its documentation for academic purposes is hereby granted without
fee,
> ##  provided that the above copyright notice appear in all copies and that
> ##  both that copyright notice and this permission notice appear in
> ##  supporting documentation, and that the name of John Overington or Mark
> ##  Johnson or our respective institutions
> ##  not be used in advertising or publicity pertaining to distribution of
> ##  the software without specific, written prior permission. We
> ##  makes no representations about the suitability of this software for any
> ##  purpose. It is provided "as is" without express or implied warranty.
> ##
> ##  JOHN OVERINGTON  AND MARK JOHNSON DISCLAIM ALL WARRANTIES WITH REGARD TO
> ##  THIS SOFTWARE/DATA, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND
> ##  FITNESS, IN NO EVENT SHALL OUR HOME INSTITUTIONS BE LIABLE FOR ANY
SPECIAL,
> ##  INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
>FROM
> ##  LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
NEGLIGENCE
> ##  OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
> ##  OR PERFORMANCE OF THIS SOFTWARE.
> ##
> ##  Primary authors:
> ##  	Dr. John Overington
> ##      Pfizer Central Research
> ##  	Pfizer UK
> ##  	Sandwich, Kent, UK
> ##
> ##  	jpo@sandwich.pfizer.com
> ##
> ##	Dr. Mark Johnson
> ##	Turku Center for Biotechnology
> ##	University of Turku & Abo Akademi University
> ##	PO Box 123
> ##	FIN-20521 Turku, Finland
> ##
> ##	mark@hops.btk.utu.fi
> ##
> ## Please send any improvements, bug fixes, useful modifications, and
comments
> ## to one of the addresses above
> */
>
>
> #define MAT_VER	"[matrix version 11.0 (last update: 24-11-95)]"
> #define MAX_MAT 15	/* Limit to matrices in mat10.h */
> #define MAX_VAL 21	/* Limit to dimensions in mat10.h */
>
> /*
>  *	B -> D (2); Z -> E (3); X (unknown) -> 21 == 0's in matrix
>  */
>
> int ind[MAX_IND]={ 0, 2, 1, 2, 3, 4, 5, 6, 7,21, 8, 9,10,
>                   11,21,12,13,14,15,16,21,17,18,21,19, 3};
>
> /*
> values in matrices are in alphabetical order (with the exception of X):
> 	ACDEFGHIKLMNPQRSTVWYX
>
> border of matrices: }, {
> */
>
> char m_names[MAX_MAT][MAX_CDE]=
>
> {"STRMAT110", "DAYHOFF", "DOOLITTLE", "FITCH", "GRANTHAM",
> "LEVIN", "MCLACHLAN", "MIYATA", "RAO", "RISLER", "GONNET",
> "HENIKOFF", "JONES", "PAM120", "TEST MATRIX"};
>
> /* m_100: scaled matrices; matrices follow in above order */
>
>
> int mats[MAX_MAT][MAX_VAL][MAX_VAL] = {
> {
> {65,10,43,45,37,45,38,38,44,38,42,42,45,43,38,46,44,46,30,35,0},
> {10,100, 7,16,20,11,18,14,11,14,19,20, 0,17,24,14,14,11,19,17,0},
> {43, 7,72,53,27,41,43,28,43,25,29,54,43,44,37,45,41,32,28,35,0},
> {45,16,53,72,31,40,43,33,48,31,37,45,42,53,43,41,42,36,28,35,0},
> {37,20,27,31,77,24,42,48,30,51,47,33,30,31,31,30,31,43,50,58,0},
> {45,11,41,40,24,71,37,24,37,25,29,42,36,35,37,41,33,29,31,32,0},
> {38,18,43,43,42,37,83,31,47,36,39,51,37,50,46,39,38,35,35,47,0},
> {38,14,28,33,48,24,31,72,32,53,54,33,33,30,32,32,40,58,36,40,0},
> {44,11,43,48,30,37,47,32,68,37,40,47,40,50,56,42,45,37,31,34,0},
> {38,14,25,31,51,25,36,53,37,68,59,32,33,37,38,30,35,51,39,39,0},
> {42,19,29,37,47,29,39,54,40,59,79,36,27,42,35,34,40,48,47,40,0},
> {42,20,54,45,33,42,51,33,47,32,36,70,41,44,45,49,46,33,31,41,0},
> {45, 0,43,42,30,36,37,33,40,33,27,41,77,37,37,42,40,35,25,32,0},
> {43,17,44,53,31,35,50,30,50,37,42,44,37,74,47,41,41,37,28,31,0},
> {38,24,37,43,31,37,46,32,56,38,35,45,37,47,76,42,42,35,37,36,0},
> {46,14,45,41,30,41,39,32,42,30,34,49,42,41,42,66,52,34,27,36,0},
> {44,14,41,42,31,33,38,40,45,35,40,46,40,41,42,52,68,42,23,34,0},
> {46,11,32,36,43,29,35,58,37,51,48,33,35,37,35,34,42,68,30,36,0},
> {30,19,28,28,50,31,35,36,31,39,47,31,25,28,37,27,23,30,91,52,0},
> {35,17,35,35,58,32,47,40,34,39,40,41,32,31,36,36,34,36,52,78,0},
> {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},
> },{ /*dayhoff*/
> {40,24,32,32,16,36,28,28,28,24,28,32,36,32,24,36,36,32,8,20,0},
> {24,80,12,12,16,20,20,24,12,8,12,16,20,12,16,32,24,24,0,32,0},
> {32,12,48,44,8,36,36,24,32,16,20,40,28,40,28,32,32,24,4,16,0},
> {32,12,44,48,12,32,36,24,32,20,24,36,28,40,28,32,32,24,4,16,0},
> {16,16,8,12,68,12,24,36,12,40,32,16,12,12,16,20,20,28,32,60,0},
> {36,20,36,32,12,52,24,20,24,16,20,32,28,28,20,36,32,28,4,12,0},
> {28,20,36,36,24,24,56,24,32,24,24,40,32,44,40,28,28,24,20,32,0},
> {28,24,24,24,36,20,24,52,24,40,40,24,24,24,24,28,32,48,12,28,0},
> {28,12,32,32,12,24,32,24,52,20,32,36,28,36,44,32,32,24,20,16,0},
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> {39,29,25,27,15,29,23,23,25,21,23,25,28,26,24,32,30,27,8,15,0},
> {29,86,10,11,23,16,20,21,12,19,22,18,11,14,15,27,24,27,22,24,0},
> {25,10,51,41,4,27,29,7,29,6,11,38,23,31,25,29,27,12,0,12,0},
> {27,11,41,45,7,23,29,13,33,12,16,31,24,36,29,28,26,17,5,13,0},
> {15,23,4,7,63,0,26,32,10,37,35,11,7,13,10,12,15,27,45,53,0},
> {29,16,27,23,0,61,20,4,21,4,9,29,18,22,22,29,21,10,6,6,0},
> {23,20,29,29,26,20,58,15,30,17,20,33,21,33,30,26,25,16,23,38,0},
> {23,21,7,13,32,4,15,47,16,41,40,12,13,17,14,18,24,43,18,23,0},
> {25,12,29,33,10,21,30,16,43,16,20,31,24,34,41,27,27,18,9,16,0},
> {21,19,6,12,37,4,17,41,16,47,41,11,15,18,15,16,20,36,23,27,0},
> {23,22,11,16,35,9,20,40,20,41,49,15,14,22,18,20,24,35,22,26,0},
> {25,18,38,31,11,29,33,12,31,11,15,46,22,30,28,31,29,15,8,20,0},
> {28,11,23,24,7,18,21,13,24,15,14,22,66,26,22,29,27,18,1,11,0},
> {26,14,31,36,13,22,33,17,34,18,22,30,26,41,34,28,27,19,13,18,0},
> {24,15,25,29,10,22,30,14,41,15,18,28,22,34,51,26,26,16,18,18,0},
> {32,27,29,28,12,29,26,18,27,16,20,31,29,28,26,38,34,22,10,17,0},
> {30,24,27,26,15,21,25,24,27,20,24,29,27,27,26,34,40,27,9,17,0},
> {27,27,12,17,27,10,16,43,18,36,35,15,18,19,16,22,27,44,13,21,0},
> {8,22,0,5,45,6,23,18,9,23,22,8,1,13,18,10,9,13,100,48,0},
> {15,24,12,13,53,6,38,23,16,27,26,20,11,18,18,17,17,21,48,67,0},
> },{/*henikoff*/
> {53,27,13,20,13,27,13,20,20,20,20,13,20,20,20,33,27,27,7,13,0},
> {27,87,7,0,13,7,7,20,7,20,20,7,7,7,7,20,20,20,13,13,0},
> {13,7,67,40,7,20,20,7,20,0,7,33,20,27,13,27,20,7,0,7,0},
> {20,0,40,60,7,13,27,7,33,7,13,27,20,40,27,27,20,13,7,13,0},
> {13,13,7,7,67,7,20,27,7,27,27,7,0,7,7,13,13,20,33,47,0},
> {27,7,20,13,7,67,13,0,13,0,7,27,13,13,13,27,13,7,13,7,0},
> {13,7,20,27,20,13,80,7,20,7,13,33,13,27,27,20,13,7,13,40,0},
> {20,20,7,7,27,0,7,53,7,40,33,7,7,7,7,13,20,47,7,20,0},
> {20,7,20,33,7,13,20,7,60,13,20,27,20,33,40,27,20,13,7,13,0},
> {20,20,0,7,27,0,7,40,13,53,40,7,7,13,13,13,20,33,13,20,0},
> {20,20,7,13,27,7,13,33,20,40,60,13,13,27,20,20,20,33,20,20,0},
> {13,7,33,27,7,27,33,7,27,7,13,67,13,27,27,33,27,7,0,13,0},
> {20,7,20,20,0,13,13,7,20,7,13,13,73,20,13,20,20,13,0,7,0},
> {20,7,27,40,7,13,27,7,33,13,27,27,20,60,33,27,20,13,13,20,0},
> {20,7,13,27,7,13,27,7,40,13,20,27,13,33,60,20,20,7,7,13,0},
> {33,20,27,27,13,27,20,13,27,13,20,33,20,27,20,53,33,13,7,13,0},
> {27,20,20,20,13,13,13,20,20,20,20,27,20,20,20,33,60,27,13,13,0},
> {27,20,7,13,20,7,7,47,13,33,33,7,13,13,7,13,27,53,7,20,0},
> {7,13,0,7,33,13,13,7,7,13,20,0,0,13,7,7,13,7,100,40,0},
> {13,13,7,13,47,7,40,20,13,20,20,13,7,20,13,13,13,20,40,73,0},
> },{/*jones*/
> {35,20,25,20,10,30,15,25,20,20,20,25,30,20,20,30,35,30,5,10,0},
> {20,80,10,5,25,20,25,15,10,10,15,20,15,10,20,30,20,15,30,35,0},
> {25,10,50,45,0,30,25,10,25,5,10,35,15,30,20,25,20,15,0,15,0},
> {20,5,45,50,0,25,25,10,30,5,10,30,15,35,25,20,20,15,0,5,0},
> {10,25,0,0,65,0,25,25,0,35,25,10,10,5,5,15,15,25,20,50,0},
> {30,20,30,25,0,50,15,10,20,5,10,25,20,20,25,30,20,15,15,5,0},
> {15,25,25,25,25,15,55,10,30,15,15,30,25,35,35,20,20,10,10,45,0},
> {25,15,10,10,25,10,10,45,10,35,40,15,15,10,10,20,30,45,5,15,0},
> {20,10,25,30,0,20,30,10,50,10,15,30,15,35,45,20,20,10,10,10,0},
> {20,10,5,5,35,5,15,35,10,50,40,10,25,15,10,15,20,35,15,20,0},
> {20,15,10,10,25,10,15,40,15,40,55,15,15,15,15,20,25,35,10,15,0},
> {25,20,35,30,10,25,30,15,30,10,15,40,20,25,25,30,30,15,0,20,0},
> {30,15,15,15,10,20,25,15,15,25,15,20,55,25,20,30,30,20,5,10,0},
> {20,10,30,35,5,20,35,10,35,15,15,25,25,50,35,20,20,10,10,15,0},
> {20,20,20,25,5,25,35,10,45,10,15,25,20,35,50,20,20,10,25,15,0},
> {30,30,25,20,15,30,20,20,20,15,20,30,30,20,20,35,30,20,10,20,0},
> {35,20,20,20,15,20,20,30,20,20,25,30,30,20,20,30,35,25,5,10,0},
> {30,15,15,15,25,15,10,45,10,35,35,15,20,10,10,20,25,45,10,10,0},
> {5,30,0,0,20,15,10,5,10,15,10,0,5,10,25,10,5,10,100,25,0},
> {10,35,15,5,50,5,45,15,10,20,15,20,10,15,15,20,10,10,25,70,0},
> },{/*120pam*/
> {55,25,40,40,20,45,25,35,30,25,30,35,45,35,25,45,45,40,5,20,0},
> {25,85,5,5,10,20,20,25,5,5,10,15,20,5,20,40,25,25,0,35,0},
> {40,5,65,55,5,40,40,25,35,15,20,50,25,45,25,40,35,25,0,15,0},
> {40,5,55,65,5,35,35,25,35,20,25,45,30,50,25,35,30,25,0,15,0},
> {20,10,5,5,80,15,25,40,5,40,35,20,15,10,15,25,20,25,35,60,0},
> {45,20,40,35,15,65,20,20,25,15,20,40,30,25,20,45,35,30,0,10,0},
> {25,20,40,35,25,20,75,20,30,25,20,50,35,55,45,30,25,25,25,35,0},
> {35,25,25,25,40,20,20,70,25,45,45,30,25,25,30,30,40,55,10,30,0},
> {30,5,35,35,5,25,30,25,65,20,40,45,30,40,50,35,35,20,15,15,0},
> {25,5,15,20,40,15,25,45,20,65,55,20,25,30,20,20,25,45,25,30,0},
> {30,10,20,25,35,20,20,45,40,55,80,25,25,35,35,30,35,45,10,20,0},
> {35,15,50,45,20,40,50,30,45,20,25,60,30,40,35,45,40,25,20,30,0},
> {45,20,25,30,15,30,35,25,30,25,25,30,70,40,35,45,35,30,5,10,0},
> {35,5,45,50,10,25,55,25,40,30,35,40,40,70,45,30,30,25,10,15,0},
> {25,20,25,25,15,20,45,30,50,20,35,35,35,45,70,35,30,25,45,15,0},
> {45,40,40,35,25,45,30,30,35,20,30,45,45,30,35,55,50,30,30,25,0},
> {45,25,35,30,20,35,25,40,35,25,35,40,35,30,30,50,60,40,10,25,0},
> {40,25,25,25,25,30,25,55,20,45,45,25,30,25,25,30,40,65,0,25,0},
> {5,0,0,0,35,0,25,10,15,25,10,20,5,10,45,30,10,0,100,30,0},
> {20,35,15,15,60,10,35,30,15,30,20,30,10,15,15,25,25,25,30,80,0},
> },{
> /*
> ng-gp
> */
> {20,22,14,13,14,13,14,22,13,18,26,22,13,5,9,18,5,30,19,26,0},
> {22,0,-25,-22,7,-14,-18,-9,-5,-5,7,-18,-5,-9,-14,-14,-10,3,-33,-22,0},
> {14,-25,28,5,19,14,13,11,9,3,3,21,9,5,18,13,18,11,-2,6,0},
> {13,-22,5,19,3,10,18,11,21,15,1,13,5,9,26,5,22,18,7,22,0},
> {14,7,19,3,14,3,1,17,11,5,-3,-3,-22,-1,7,18,11,-3,12,28,0},
> {13,-14,14,10,3,19,-3,22,1,-1,-6,13,14,14,5,9,7,15,-1,-2,0},
> {14,-18,13,18,1,-3,30,7,17,-2,6,13,5,13,13,5,5,10,1,5,0},
> {22,-9,11,11,17,22,7,11,11,17,28,10,-1,-1,3,-2,5,3,-3,18,0},
> {13,-5,9,21,11,1,17,11,15,14,1,13,13,13,28,13,13,14,15,15,0},
> {18,-5,3,15,5,-1,-2,17,14,11,20,-1,9,11,-6,7,6,9,1,-7,0},
> {26,7,3,1,-3,-6,6,28,1,20,-3,1,-14,-3,3,11,14,17,9,5,0},
> {22,-18,21,13,-3,13,13,10,13,-1,1,28,5,13,18,17,9,19,-2,1,0},
> {13,-5,9,5,-22,14,5,-1,13,9,-14,5,26,6,14,13,14,14,-14,3,0},
> {5,-9,5,9,-1,14,13,-1,13,11,-3,13,6,19,21,14,13,18,3,7,0},
> {9,-14,18,26,7,5,13,3,28,-6,3,18,14,21,22,9,22,19,-7,-14,0},
> {18,-14,13,5,18,9,5,-2,13,7,11,17,13,14,9,24,17,7,-9,10,0},
> {5,-10,18,22,11,7,5,5,13,6,14,9,14,13,22,17,20,26,-16,14,0},
> {30,3,11,18,-3,15,10,3,14,9,17,19,14,18,19,7,26,7,6,26,0},
> {19,-33,-2,7,12,-1,1,-3,15,1,9,-2,-14,3,-7,-9,-16,6,5,9,0},
> {26,-22,6,22,28,-2,5,18,15,-7,5,1,3,7,-14,10,14,26,9,18,0},},};
>
>
>
> /*
> 65families
> {62,27,35,38,27,38,31,31,38,27,38,35,38,38,38,42,38,38,23,27,0},
> {27,100,0,23,27,4,12,15,19,0,8,8,0,19,27,12,12,15,12,8,0},
> {35,0,73,50,12,35,42,23,31,8,19,54,38,38,31,42,38,19,12,27,0},
> {38,23,50,69,12,35,31,23,46,15,27,42,38,50,46,35,42,31,12,31,0},
> {27,27,12,12,81,8,35,46,23,50,38,19,15,19,19,23,27,38,54,58,0},
> {38,4,35,35,8,69,27,15,27,12,23,38,35,31,31,38,27,19,19,23,0},
> {31,12,42,31,35,27,88,19,42,19,35,50,23,42,42,31,27,31,31,38,0},
> {31,15,23,23,46,15,19,73,23,50,50,27,19,12,19,23,31,54,31,35,0},
> {38,19,31,46,23,27,42,23,69,31,38,42,38,46,58,38,38,27,27,31,0},
> {27,0,8,15,50,12,19,50,31,69,58,23,27,23,23,19,23,46,38,31,0},
> {38,8,19,27,38,23,35,50,38,58,81,31,15,46,15,15,31,42,35,35,0},
> {35,8,54,42,19,38,50,27,42,23,31,69,27,38,35,46,42,15,12,35,0},
> {38,0,38,38,15,35,23,19,38,27,15,27,81,31,35,35,35,19,19,12,0},
> {38,19,38,50,19,31,42,12,46,23,46,38,31,73,50,38,38,31,15,27,0},
> {38,27,31,46,19,31,42,19,58,23,15,35,35,50,77,38,38,27,31,35,0},
> {42,12,42,35,23,38,31,23,38,19,15,46,35,38,38,62,50,27,12,31,0},
> {38,12,38,42,27,27,27,31,38,23,31,42,35,38,38,50,65,35,15,31,0},
> {38,15,19,31,38,19,31,54,27,46,42,15,19,31,27,27,35,65,15,35,0},
> {23,12,12,12,54,19,31,31,27,38,35,12,19,15,31,12,15,15,96,54,0},
> {27,8,27,31,58,23,38,35,31,31,35,35,12,27,35,31,31,35,54,81,0},
> */
>-- End of excerpt from Mark Johnson MOL


______________________________________________________________________________


On Sep 16, 11:08am, Adam Godzik wrote:
>
> Tomii K., Kanehisa M. (1996) Prot. Eng. 9:27-36
> Vogt G., Etzold T., Argos P. (1995) J. Mol. Biol. 249:816-831
>
> the web site with all the matrices - http://www.genome.ad.jp
>
> Adam
>-- End of excerpt from Adam Godzik


______________________________________________________________________________



On Sep 16, 11:48am, Adam Godzik wrote:
>
> You can find and download the indexes database by
> ftp'ing to ftp.genome.ad.jp and cd'ing to /db/genomenet/aaindex
>
>
> Adam
>-- End of excerpt from Adam Godzik


______________________________________________________________________________



On Sep 17,  3:52pm, Malcolm Cline wrote:
> Subject: homology matrices
>
> SYBYL contains six of them--Dayhoff, SwissProt, Identity, APG, Greer,
> and a physical property matrix.  If you do not have our software,
> drop me a line and I will mail copies of the matrices to you.
>
> mac
> Malcolm A. Cline
> Senior Marketing Scientist
> Tripos, Inc.
>-- End of excerpt from Malcolm Cline


______________________________________________________________________________



On Sep 17,  4:43pm, Malcolm Cline wrote:
> Subject: Re: homology matrices
>
> APG:
>
> 24
> ABCDEFHIKLMNQRSTVWYZPGX-
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
> Note: A dash (-) represents a gap.
>
>
>
> Greer:
>
> 24
> ACDEFGHIKLMNPQRSTVWYBXZ-
> 1  0  0  0  0  .5 0  .5 0  .5 0  0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
> 0  0  1  .5 0  0  0  0  .5 0  0  0  0  0  .5 0  0  0  0  0  1  0  .5 0
> 0  0  .5 1  0  0  0  0  .5 0  0  0  0  0  .5 0  0  0  0  0  .5 0  1  0
> 0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  .5 .5 0  0  0  0
> .5 0  0  0  0  1  0  0  0  0  0  0  .5 0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
> .5 0  0  0  0  0  0  1  0  .5 .5 0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  .5 .5 0  0  0  0  1  0  0  0  0  0  .5 0  0  0  0  0  .5 0  .5 0
> .5 0  0  0  0  0  0  .5 0  1  .5 0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  0  .5 0  .5 1  0  0  0  0  0  0  .5 0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  1  0  .5 0  0  0  0  0  0  1  0  .5 0
> 0  0  0  0  0  .5 0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  .5 0  1  0  0  0  0  0  0  .5 0  1  0
> 0  0  .5 .5 0  0  0  0  .5 0  0  0  0  0  1  0  0  0  0  0  .5 0  .5 0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  .5 0  0  0  0  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  .5 1  0  0  0  0  0  0  0
> .5 0  0  0  0  .5 0  .5 0  .5 .5 0  0  0  0  0  0  1  0  0  0  0  0  0
> 0  0  0  0  .5 0  0  0  0  0  0  0  0  0  0  0  0  0  1  .5 0  0  0  0
> 0  0  0  0  .5 0  0  0  0  0  0  0  0  0  0  0  0  0  .5 1  0  0  0  0
> 0  0  1  .5 0  0  0  0  .5 0  0  1  0  .5 .5 0  0  0  0  0  1  0  0  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0
> 0  0  .5 1  0  0  0  0  .5 0  0  .5 0  1  .5 0  0  0  0  0  0  0  1  0
> 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
>
>
>
> Identity:
>
> 24
> ACDEFGHIKLMNPQRSTVWYBXZ-
>  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
>
> Note: A dash (-) represents a gap.
>
>
>
>
> Physical Properties:
>
> ARNDCQEGHILKMFPSTWYVBZX-
>    1.000  -0.351  -0.166   0.085  -0.260   0.231   0.589  -0.034   0.345
  0.023
>    0.386   0.019   0.482  -0.139  -0.484  -0.104  -0.182  -0.485  -0.857
  0.126
>    0.085   0.589   0.000   0.000
>   -0.351   1.000   0.450   0.552  -0.570   0.623   0.465  -0.060   0.473
 -0.540
>   -0.583   0.813  -0.406  -0.493  -0.011   0.136   0.010  -0.234  -0.091
 -0.526
>    0.552   0.465   0.000   0.000
>   -0.166   0.450   1.000   0.866  -0.243   0.387   0.235   0.811   0.020
 -0.928
>   -0.901   0.530  -0.856  -0.845   0.500   0.788   0.215  -0.531  -0.238
 -0.854
>    0.866   0.235   0.000   0.000
>    0.085   0.552   0.866   1.000  -0.493   0.458   0.589   0.632   0.184
 -0.915
>   -0.761   0.770  -0.702  -0.850   0.312   0.575  -0.063  -0.615  -0.517
 -0.876
>    1.000   0.589   0.000   0.000
>   -0.260  -0.570  -0.243  -0.493   1.000  -0.611  -0.809   0.203  -0.589
  0.424
>    0.107  -0.776   0.035   0.311   0.179   0.169   0.376   0.253   0.424
  0.448
>   -0.493  -0.809   0.000   0.000
>    0.231   0.623   0.387   0.458  -0.611   1.000   0.592  -0.031   0.573
 -0.493
>   -0.369   0.645  -0.088  -0.571  -0.394   0.185   0.231  -0.519  -0.481
 -0.356
>    0.458   0.592   0.000   0.000
>    0.589   0.465   0.235   0.589  -0.809   0.592   1.000  -0.113   0.761
 -0.496
>   -0.080   0.768   0.102  -0.428  -0.344  -0.105  -0.459  -0.445  -0.803
 -0.483
>    0.589   1.000   0.000   0.000
>   -0.034  -0.060   0.811   0.632   0.203  -0.031  -0.113   1.000  -0.421
 -0.637
>   -0.717   0.047  -0.794  -0.707   0.632   0.893   0.388  -0.561  -0.196
 -0.525
>    0.632  -0.113   0.000   0.000
>    0.345   0.473   0.020   0.184  -0.589   0.573   0.761  -0.421   1.000
 -0.295
>    0.049   0.520   0.356  -0.139  -0.477  -0.263  -0.363  -0.129  -0.499
 -0.270
>    0.184   0.761   0.000   0.000
>    0.023  -0.540  -0.928  -0.915   0.424  -0.493  -0.496  -0.637  -0.295
  1.000
>    0.847  -0.718   0.729   0.854  -0.419  -0.662  -0.032   0.526   0.392
  0.944
>   -0.915  -0.496   0.000   0.000
>    0.386  -0.583  -0.901  -0.761   0.107  -0.369  -0.080  -0.717   0.049
  0.847
>    1.000  -0.507   0.920   0.849  -0.604  -0.842  -0.429   0.505   0.056
  0.740
>   -0.761  -0.080   0.000   0.000
>    0.019   0.813   0.530   0.770  -0.776   0.645   0.768   0.047   0.520
 -0.718
>   -0.507   1.000  -0.379  -0.571  -0.013   0.088  -0.307  -0.295  -0.393
 -0.769
>    0.770   0.768   0.000   0.000
>    0.482  -0.406  -0.856  -0.702   0.035  -0.088   0.102  -0.794   0.356
  0.729
>    0.920  -0.379   1.000   0.709  -0.782  -0.798  -0.348   0.359  -0.125
  0.687
>   -0.702   0.102   0.000   0.000
>   -0.139  -0.493  -0.845  -0.850   0.311  -0.571  -0.428  -0.707  -0.139
  0.854
>    0.849  -0.571   0.709   1.000  -0.336  -0.829  -0.409   0.858   0.544
  0.664
>   -0.850  -0.428   0.000   0.000
>   -0.484  -0.011   0.500   0.312   0.179  -0.394  -0.344   0.632  -0.477
 -0.419
>   -0.604  -0.013  -0.782  -0.336   1.000   0.629   0.234  -0.059   0.359
 -0.414
>    0.312  -0.344   0.000   0.000
>   -0.104   0.136   0.788   0.575   0.169   0.185  -0.105   0.893  -0.263
 -0.662
>   -0.842   0.088  -0.798  -0.829   0.629   1.000   0.669  -0.692  -0.181
 -0.451
>    0.575  -0.105   0.000   0.000
>   -0.182   0.010   0.215  -0.063   0.376   0.231  -0.459   0.388  -0.363
 -0.032
>   -0.429  -0.307  -0.348  -0.409   0.234   0.669   1.000  -0.481   0.118
  0.236
>   -0.063  -0.459   0.000   0.000
>   -0.485  -0.234  -0.531  -0.615   0.253  -0.519  -0.445  -0.561  -0.129
  0.526
>    0.505  -0.295   0.359   0.858  -0.059  -0.692  -0.481   1.000   0.749
  0.258
>   -0.615  -0.445   0.000   0.000
>   -0.857  -0.091  -0.238  -0.517   0.424  -0.481  -0.803  -0.196  -0.499
  0.392
>    0.056  -0.393  -0.125   0.544   0.359  -0.181   0.118   0.749   1.000
  0.252
>   -0.517  -0.803   0.000   0.000
>    0.126  -0.526  -0.854  -0.876   0.448  -0.356  -0.483  -0.525  -0.270
  0.944
>    0.740  -0.769   0.687   0.664  -0.414  -0.451   0.236   0.258   0.252
  1.000
>   -0.876  -0.483   0.000   0.000
>    0.085   0.552   0.866   1.000  -0.493   0.458   0.589   0.632   0.184
 -0.915
>   -0.761   0.770  -0.702  -0.850   0.312   0.575  -0.063  -0.615  -0.517
 -0.876
>    1.000   0.589   0.000   0.000
>    0.589   0.465   0.235   0.589  -0.809   0.592   1.000  -0.113   0.761
 -0.496
>   -0.080   0.768   0.102  -0.428  -0.344  -0.105  -0.459  -0.445  -0.803
 -0.483
>    0.589   1.000   0.000   0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
  0.000
>    0.000   0.000   0.000   0.000
>
>
>
>
> SwissProt:
>
> 24
> CSTPAGNDEQHRKMILVFYWBZX-
>  11.5  0.1 -0.5 -3.1  0.5 -2.0 -1.8 -3.2 -3.0 -2.4 -1.3 -2.2 -2.8 -0.9 -1.1
-1.5  0.0 -0.8 -0.5 -1.0 -3.2 -3.0  0.0  0.0
>   0.1  2.2  1.5  0.4  1.1  0.4  0.9  0.5  0.2  0.2 -0.2 -0.2  0.1 -1.4 -1.8
-2.1 -1.0 -2.8 -1.9 -3.3  0.5  0.2  0.0  0.0
>  -0.5  1.5  2.5  0.1  0.6 -1.1  0.5  0.0 -0.1  0.0 -0.3 -0.2  0.1 -0.6 -0.6
-1.3  0.0 -2.2 -1.9 -3.5  0.0 -0.1  0.0  0.0
>  -3.1  0.4  0.1  7.6  0.3 -1.6 -0.9 -0.7 -0.5 -0.2 -1.1 -0.9 -0.6 -2.4 -2.6
-2.3 -1.8 -3.8 -3.1 -5.0 -0.7 -0.5  0.0  0.0
>   0.5  1.1  0.6  0.3  2.4  0.5 -0.3 -0.3  0.0 -0.2 -0.8 -0.6 -0.4 -0.7 -0.8
-1.2  0.1 -2.3 -2.2 -3.6 -0.3  0.0  0.0  0.0
>  -2.0  0.4 -1.1 -1.6  0.5  6.6  0.4  0.1 -0.8 -1.0 -1.4 -1.0 -1.1 -3.5 -4.5
-4.4 -3.3 -5.2 -4.0 -4.0  0.1 -0.8  0.0  0.0
>  -1.8  0.9  0.5 -0.9 -0.3  0.4  3.8  2.2  0.9  0.7  1.2  0.3  0.8 -2.2 -2.8
-3.0 -2.2 -3.1 -1.4 -3.6  2.2  0.9  0.0  0.0
>  -3.2  0.5  0.0 -0.7 -0.3  0.1  2.2  4.7  2.7  0.9  0.4 -0.3  0.5 -3.0 -3.8
-4.0 -2.9 -4.5 -2.8 -5.2  4.7  2.7  0.0  0.0
>  -3.0  0.2 -0.1 -0.5  0.0 -0.8  0.9  2.7  3.6  1.7  0.4  0.4  1.2 -2.0 -2.7
-2.8 -1.9 -3.9 -2.7 -4.3  2.7  3.6  0.0  0.0
>  -2.4  0.2  0.0 -0.2 -0.2 -1.0  0.7  0.9  1.7  2.7  1.2  1.5  1.5 -1.0 -1.9
-1.6 -1.5 -2.6 -1.7 -2.7  0.9  1.7  0.0  0.0
>  -1.3 -0.2 -0.3 -1.1 -0.8 -1.4  1.2  0.4  0.4  1.2  6.0  0.6  0.6 -1.3 -2.2
-1.9 -2.0 -0.1  2.2 -0.8  0.4  0.4  0.0  0.0
>  -2.2 -0.2 -0.2 -0.9 -0.6 -1.0  0.3 -0.3  0.4  1.5  0.6  4.7  2.7 -1.7 -2.4
-2.2 -2.0 -3.2 -1.8 -1.6 -0.3  0.4  0.0  0.0
>  -2.8  0.1  0.1 -0.6 -0.4 -1.1  0.8  0.5  1.2  1.5  0.6  2.7  3.2 -1.4 -2.1
-2.1 -1.7 -3.3 -2.1 -3.5  0.5  1.2  0.0  0.0
>  -0.9 -1.4 -0.6 -2.4 -0.7 -3.5 -2.2 -3.0 -2.0 -1.0 -1.3 -1.7 -1.4  4.3  2.5
 2.8  1.6  1.6 -0.2 -1.0 -3.0 -2.0  0.0  0.0
>  -1.1 -1.8 -0.6 -2.6 -0.8 -4.5 -2.8 -3.8 -2.7 -1.9 -2.2 -2.4 -2.1  2.5  4.0
 2.8  3.1  1.0 -0.7 -1.8 -3.8 -2.7  0.0  0.0
>  -1.5 -2.1 -1.3 -2.3 -1.2 -4.4 -3.0 -4.0 -2.8 -1.6 -1.9 -2.2 -2.1  2.8  2.8
 4.0  1.8  2.0  0.0 -0.7 -4.0 -2.8  0.0  0.0
>   0.0 -1.0  0.0 -1.8  0.1 -3.3 -2.2 -2.9 -1.9 -1.5 -2.0 -2.0 -1.7  1.6  3.1
 1.8  3.4  0.1 -1.1 -2.6 -2.9 -1.9  0.0  0.0
>  -0.8 -2.8 -2.2 -3.8 -2.3 -5.2 -3.1 -4.5 -3.9 -2.6 -0.1 -3.2 -3.3  1.6  1.0
 2.0  0.1  7.0  5.1  3.6 -4.5 -3.9  0.0  0.0
>  -0.5 -1.9 -1.9 -3.1 -2.2 -4.0 -1.4 -2.8 -2.7 -1.7  2.2 -1.8 -2.1 -0.2 -0.7
 0.0 -1.1  5.1  7.8  4.1 -2.8 -2.7  0.0  0.0
>  -1.0 -3.3 -3.5 -5.0 -3.6 -4.0 -3.6 -5.2 -4.3 -2.7 -0.8 -1.6 -3.5 -1.0 -1.8
-0.7 -2.6  3.6  4.1 14.2 -5.2 -4.3  0.0  0.0
>  -3.2  0.5  0.0 -0.7 -0.3  0.1  2.2  4.7  2.7  0.9  0.4 -0.3  0.5 -3.0 -3.8
-4.0 -2.9 -4.5 -2.8 -5.2  0.0  0.0  0.0  0.0
>  -3.0  0.2 -0.1 -0.5  0.0 -0.8  0.9  2.7  3.6  1.7  0.4  0.4  1.2 -2.0 -2.7
-2.8 -1.9 -3.9 -2.7 -4.3  0.0  0.0  0.0  0.0
>   0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
>   0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
>
> Swiss Mutation Matrix
> Gaston H.Gonnet, Mark A.Cohen, Steven A. Benner,
> Exhaustive Matching of the Entire Protein Sequence Database,
> Science, 5 June 92, 256, pp. 1443-1445.
> Min =  -5.2  Max =  14.2  Ave =  -0.4
> Recommended gap penalty = 6.
>
>
>
> Since you already have Dayhoff, I am not sending it.  Hope these help!
>
> mac
>-- End of excerpt from Malcolm Cline


______________________________________________________________________________

-- 
Dimitris K. Agrafiotis, PhD              | e-mail: dimitris@3dp.com
3-Dimensional Pharmaceuticals, Inc.      | tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | fax:    (610) 458-8249
Exton, PA 19341



From schneider@msbcs.ENET.dec.com  Fri Sep 27 16:58:16 1996
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Date: Fri, 27 Sep 96 16:36:10 EDT
From: "Chuck (aka chazix), 508-493-1399 (DTN 223-1399)  27-Sep-1996 1545 -0400" 
To: chemistry@www.ccl.net
Cc: loh@msbcs.ENET.dec.com, schneider@msbcs.ENET.dec.com
Subject: re: CCL:f77 comp. on DEC alpha




Greetings,

I'm not usually a follower of this forum, but a colleague asked me if I could
respond to Rochus Schmid's inquiry about building deMon for an Alpha system. 
I will assume that the operating system is Digital UNIX.

I wouldn't say unaligned accesses are common when porting Fortran code to the
Alpha architecture, but they can certainly happen.  I can only make rather
general statements about what sort of code contructs cause unaligned accesses.
By default, the compiler assumes that data are stored at addresses that are a
multiple of the size of the data type - for example, INTEGER*4 data is
expected to be at an address that is a multiple of 4.  If this assumption is
broken, unaligned accesses are likely.  I would say that the easiest way for
this to happen in pure Fortran code is a mismatch between the data types of
the formal and actual parameters of a subroutine call - for example, passing a
REAL*4 argument to a subroutine that expects an REAL*8.

I would not assume that the problem is related to the 64-bit nature of the
Alpha architecture, since standard Fortran constructs don't have any notion of
the size of an address (as far as I can think of at the moment).  However, if
there is any use of POINTER types, or any non-Fortran code involved, there are
more possibilities for introducing unaligned accesses.

The statement that the program stops at the time of the unaligned access
puzzles me.  The operating system will "fix up" unaligned accesses so that
the access completes, albeit at a tremendous cost to performance.  It seems
more likely that the unaligned access is just the first symptom of a problem
that eventually results in the halt.  The program may stop so quickly after
the unaligned access that it appears to be simultaneous, but I would expect an
additional message about what actually stops the program - for example,
"signal segmentation fault".

To determine what's causing an unaligned access, one way is to disable the
operating system "fixup", so that the unaligned access will result in the
program being signaled.  The signal can be caught while running the program
under a debugger, or the program can be simply be run and allowed to dump a
core file upon receiving the signal, after which the core file can be examined
with a debugger.  For example, given a program named a.out:

$ uac p sigbus		! make unaligned access cause SIGBUS (see man 1 uac)
$ a.out			! run program
  (core dumped)
$ dbx a.out core	! use debugger to analyze core dump
dbx> where
$ uac p reset		! reset unaligned accesses to being fixed up

Regards,
Chuck Schneider
Digital High Performance Computing Expertise Center, Maynard, Massachusetts


From owner-chemistry@ccl.net  Wed Sep 25 14:00:28 1996
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From: "Emadeddin Tajkhorshid" 
Message-Id: <9609251845.ZM11163@mbp-sgi7.inet.dkfz-heidelberg.de>
Date: Wed, 25 Sep 1996 18:45:12 +0100
Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de
X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail)
To: chemistry@ccl.net (Computational Chemistry List)
Subject: Freezing a number of atoms in G94



Dear CCLers

I want to know if it is possible to freeze a number of atoms in their cartesian
coordinates during G94 geometry optimization.

many thanx

-- 
Emad
*********************************************************************
E. Tajkhorshid				
German Cancer Research Center; DKFZ  Tel: +49 6221 42 2339
Dept. Molecular Biophysics (0810)    FAX: +49 6221 42 2333
P.O.Box 101949			   Email: E.Tajkhorshid@DKFZ-Heidelberg.DE
69009 Heidelberg, FRG
***********************************************************************
* A friend may well be reckoned a masterpiece of the nature (Emerson) *
***********************************************************************


From ccl@www.ccl.net  Sun Sep 29 18:58:37 1996
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From: Anthony P Scott 
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Date: Mon, 30 Sep 1996 08:26:16 +1000 (EST)
To: chemistry@ccl.net
Subject: Harmonic Vibrational Frequencies
Message-ID: 




Dear Colleague,

Over the last year or so many questions have been asked about suitable 
scaling factors that may be applied to calculated harmonic vibrational 
frequencies in order to obtain fundamental vibrational frequencies.

We are pleased to announce that our paper on this subject has been 
accepted and will be in print soon. The paper:

Harmonic Vibrational Frequencies: An Evaluation of Hartree-Fock, 
Moller-Plesset, Quadratic Configuration Interaction, Density Functional 
Theory and Semiempirical Scale Factors
Anthony P. Scott and Leo Radom, 
J. Phys. Chem., 100, 16502, (1996) 

presents scale factors for obtaining:

1. fundamental vibrational frequencies 
2. low frequency vibrations
3. zero-point vibrational energies
4. thermal contributions to:
    a) enthalpy 
    b) entropy 

>from harmonic frequencies determined at 19 levels of theory.

The levels of theory are:

AM1 and PM3 (fundamental vibrational frequencies only)
HF/3-21G
HF/6-31G(d)
HF/6-31+G(d)
HF/6-31G(d,p)
HF/6-311G(d,p)
HF/6-311G(df,p)
MP2-fu/6-31G(d)
MP2-fc/6-31G(d)
MP2-fc/6-31G(d,p)
MP2-fc/6-311G(d,p)
QCISD/6-31G(d)

B-LYP/6-31G(d)
B-LYP/6-311G(df,p)
B-P86/6-31G(d)
B3-LYP/6-31G(d)
B3-P86/6-31G(d)
B3-PW91/6-31G(d)

We hope that this paper will prove useful to you.

Kind Regards,

Tony Scott



From ccl@www.ccl.net  Tue Oct  1 05:13:17 1996
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Date: Tue, 1 Oct 1996 10:38:44 +0200 (MESZ)
From: Thomas Nowak 
To: CHEMISTRY@ccl.net
Subject: CCL: G94 Problem after updating the OS
Message-Id: 




Hi,

We have a little problem after updating our system (RS6000) form AIX 3.2 to
AIX 4.1. Now our Gaussian94 (compiled with AIX3.2) breaks with a message:

lock-new-file: No locks available
fname=/u/cm/cmral/G94/tmp/g94-14908.rwf
lock-new-file

Can everybody tell me if that is a problem of configuration of AIX or of 
G94. Must I really recompile the programm?

Thanks

Thomas




From owner-chemistry@ccl.net  Wed Sep 25 15:00:18 1996
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	id AA19258; Wed, 25 Sep 1996 13:54:21 -0400
Date: Wed, 25 Sep 1996 13:54:21 -0400 (EDT)
From: "Stephen R. Heller" 
To: jcicshelp , chemistry@ccl.net,
        chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu
Cc: ken@softshell.com, "Stephen R. Heller" 
Subject: Software for Review
Message-Id: 





Subject: Software and Database for Review

September 25, 1996

Subject:  Computer Software for Review

     As the Software Review Editor for the ACS Journal of
Chemical Information and Computer Science (JCICS) I often get
software for review in the journal.   I have 2 new software and
database products. I am looking for people who are willing to
review these software/databases products.  In return for the
review which is published in JCICS you get to keep the software
or database.  The review should be completed in 1-3 months.  The
length of the review is 4-10 double spaced typed pages.  Sample
reviews can be found in most of the recent issues of JCICS.

     Please try to give me some (short) reason to choose you over
another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE
AVAILABLE.  Messages with such replies are trashed!

     I have tried this approach for about the past five years and
it is working reasonably well. (REMINDER: For those who haven't
finished your reviews of software sent months and months ago,
this last sentence does not apply to you!)  As a result, I am
continuing this new method to find reviewers using this e-
mail/user group system.  I reserve the right to abandon this if
it is a problem, or inappropriate.  I will not notify people if I
have found a reviewer.  If you don't hear from me within a few
days I have chosen someone else to review the particular package.

     As I get many, many, (too many) replies to this message,
please do not respond after 26 September 1995 (Thursday), as I am
sure the software will be gone by then.

     I can be reached on Internet (SRHELLER@GIG.US.GOV).

     PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX
NUMBER!!!  (I send the software by Federal Express.)  Without
this information I WILL NOT consider your request.


     Steve Heller


The packages I now have are:

1. Chemwindows DB 4.0, a chemical structure drawing program from
Softshell.  For Windows 95/NT only.

2. SymApps 1.0, a program to calculate and display symmetry point
groups.  Also used for visualization (4 different styles)and high-
quality publishing.  For Windows 95/NT only.

Steve Heller, USDA, ARS, Plant Genome Project
Bldg. 005, Room 337
Beltsville, MD 20705-2350 USA
Phone: 301-504-6055   FAX: 301-504-6231
E-mail:  srheller@gig.usda.gov
WWW:     www.hellers.com/~steve



From ccl@www.ccl.net  Tue Oct  1 15:13:23 1996
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Message-ID: <32517754.6B8B@rutchem.rutgers.edu>
Date: Tue, 01 Oct 1996 14:56:23 -0500
From: "Ronald R. Sauers" 
Reply-To: sauers@rutchem.rutgers.edu
Organization: Rutgers University
X-Mailer: Mozilla 3.0 (Macintosh; I; PPC)
To: CHEMISTRY@ccl.net
Subject: IGLO-Where can I find it?




I am trying to locate the IGLO program to do some magnetic
susceptibility, chemical shift calculations, etc. Can someone tell me
how to gain access to it?

Thanks,

rrsauers


From qojskd@uscmail.usc.es  Tue Oct  1 05:13:22 1996
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	id AA14922; Tue, 1 Oct 1996 10:17:21 +0100
Date: Tue, 1 Oct 1996 10:17:21 +0100
Message-Id: <199610010917.AA14922@uscmail.usc.es>
From: "F. Javier Sardina"  
To: CHEMISTRY@www.ccl.net
Subject: Freeware for NMR data processing on PC's



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



From owner-chemistry@ccl.net  Thu Sep 26 11:58:12 1996
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From: siroiss@CHIMCN.UMontreal.CA (Sirois Suzanne)
Message-Id: <199609261540.LAA18079@chims1.CHIMCN.UMontreal.CA>
Subject: Malonaldehyde
To: chemistry@ccl.net
Date: Thu, 26 Sep 1996 11:40:20 -0400 (EDT)




Dear Netters, 
	I'm looking for the bes post-HF and DFT calculations 
of malonaldehyde (structural parameters, vibrational analysis and
internal proton transfer energy barrier).

	Thanks,
	
*************************************************
*  Dr. Suzanne Sirois                           *
*  Office  CERCA                                *
*  Theoretical Chemistry Groups                 *
*  Department of Chemistry                      *
*  University of Montreal                       *
*  C.P. 6128, Succ Centre-Ville                 *
*  Montreal, Quebec H3C 3J7                     *
*  Canada                                       *
*                                               *
*  tel: (514) 369-5228                          *
*  Fax  (514) 369-3880                          *
*  e-mail: siroiss@cerca.umontreal.ca           *
*  e-mail: siroiss@chimcn.umontreal.ca          *
*  fax: (514) 343-2468                          *
*************************************************



From ccl@www.ccl.net  Tue Oct  1 12:13:23 1996
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From: 
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Date: Tue, 01 Oct 1996 16:53:18 MET-DST
To: CHEMISTRY@ccl.net





Dear Netters,

where can I find out or how can I generate the torsional paremeters
for 3-2-2-6 dihedral angle in Allinger's MM3(92)? 3 is Csp2 
carbonyl, 2 is Csp2 alkene, and 6 is O from C-O-H. I shall 
appreciate any help or suggestion



Rudolf

----------------------------
Rudolf Kiralj
Rudjer Boskovic Institute
P.O.B. 1016
HR-10001 Zagreb, Croatia
e-mail: kiralj@olimp.irb.hr
----------------------------




From saarela@messi.uku.fi  Wed Sep 25 05:31:21 1996
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	by www.ccl.net (8.7.5/950822.1) id FAA08474; Wed, 25 Sep 1996 05:31:16 -0400 (EDT)
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          id AA55347; Wed, 25 Sep 1996 12:30:55 +0300
From: saarela@messi.uku.fi (Janne Saarela)
Message-Id: <9609250930.AA55347@messi.uku.fi>
Subject: ANNOUNCE: Plasmid Processor software available for free!
To: chemistry@www.ccl.net
Date: Wed, 25 Sep 1996 12:30:54 +0200 (WET)




Introduction

Plasmid Processor is a simple tool for plasmid presentation for scientific and
educational purposes. It features both circular and linear DNA, user
defined restriction sites, genes and multiple cloning site. In addition you 
can manipulate plasmid by inserting and deleting fragments. Created drawings 
can be copied to clipboard or saved to disk for later use. Printing from 
withing program is also supported. 

Plasmid Processor is freeware, so you can use and distribute it freely. 

You can download full executable version of Plasmid Processor 1.02 for Windows
(tm) at URL

http://www.uku.fi/~kiviraum/plasmid/plasmid.html

( plasp102.zip (239k). )

Authors

Plasmid Processor program was created during a programming project course
organized by the Department of Computer Sciences and Applied Mathematics,
University of Kuopio, Finland 1995-1996. The program was made for the
Department of Biochemistry and Biotechnology, University of Kuopio, 
which owns the copyrights of the program. 

Programming team: T. Kivirauma, P. Oikari and J.Saarela.

For further information please contact the authors by e-mail, plasmid@uku.fi. 
Any comment on program is greatly appreciated. 

Regards,

Janne Saarela

-- 
Janne Saarela

student of BIOTECHNOLOGY, 7th grade, BSc, PhD student
University of Kuopio, FINLAND
Office:  Room 3090, Department of Chemistry
         BOX 1627
	 FIN-70211 KUOPIO
	 FINLAND
Phone:   (+358)-71-163 257
Telefax: (+358)-71-163 259
Email:   saarela@messi.uku.fi
WWW: http://www.uku.fi/~saarela/  
Home:    Mustinlammenkatu 4 B 16
         FIN-70600 Kuopio
	 FINLAND
Phone:   (+358)-71-2826 325
Mobile Phone: (+358)-50-68 001