From schmitz@mpi-dortmund.mpg.de Fri Nov 25 04:14:37 1994 Received: from ks.mpi-dortmund.mpg.de for schmitz@mpi-dortmund.mpg.de by www.ccl.net (8.6.9/930601.1506) id EAA18119; Fri, 25 Nov 1994 04:07:47 -0500 Received: by ks.mpi-dortmund.mpg.de (4.1/SMI-4.1MHS-mpi-1.4.93) id AA05055; Fri, 25 Nov 94 10:07:03 +0100 Date: Fri, 25 Nov 94 10:07:03 +0100 From: frank.schmitz@mpi-dortmund.mpg.de (F.Schmitz) Message-Id: <9411250907.AA05055@ks.mpi-dortmund.mpg.de> To: chemistry@ccl.net Subject: Email adress M. Carson Dear netters Does anybody know the email adress from Mike Carson from the university of alabama? Thank you ! Frank frank.schmitz@mpi-dortmund.mpg.de From peeter@chem.ut.ee Fri Nov 25 05:14:38 1994 Received: from Tera for peeter@chem.ut.ee by www.ccl.net (8.6.9/930601.1506) id FAA18371; Fri, 25 Nov 1994 05:08:59 -0500 Received: by Tera (Linux Smail3.1.28.1 #1) id m0rAxf2-00028QC; Fri, 25 Nov 94 12:13 EET Message-Id: From: peeter@chem.ut.ee (Peeter Burk) Subject: Gaussian benchmarks (summary) To: chemistry@ccl.net Date: Fri, 25 Nov 1994 12:13:46 +0200 (EET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 5929 Hi! Some time ago I asked on this forum about Gaussian benchmarks for different computers. However, to my astonishment I got quite a few replays. Still, if somebody have some data to, I will be most thankfull. Anyways, here comes the original inquiry and the answers I got. ______________________________________________________________________ From peeter Tue Nov 8 17:11:02 1994 Subject: Gaussian benchmark request Dear all, We have now lucky possibility to buy new workstation for our group. We will use it primarily for running gaussian (and other QM programs like this). Can somebody point me to the places in the net, where one can obtain gaussian benchmark information for various computers? When such information is not available, can you please send to me the timings of some testjobs? Please send your answers directly to me and I will later summarize for net. Best regards, Peeter ---------------------------------------------------------------------- From hommes@ccc.uni-erlangen.de Dr. N.J.R. van Eikema Hommes Computational Chemistry Center University of Erlangen Naegelsbachstrasse 25 D-91052 Erlangen, F.R.G. hommes@ccc.uni-erlangen.de Ab Initio Benchmarks Gaussian 92, Cyclohexane (D3d) Platform HF/6-31G* HF/6-31G* MP2(fu)/6-31G* MP4sdtq/6-31G* Optimization Frequencies Optimization Single Point CDC CD4680fs 4986 21172 41673 - (0.52) (0.59) (0.38) Convex C210 2570 12500 15900 33900 (1.00) (1.00) (1.00) (1.00) SGI R4000 2445 12300 24300 92700 100 MHz (1.05) (1.02) (0.65) (0.37) SGI R4400 1594 7528 15483 - 150 MHz (1.61) (1.66) (1.03) HP 730 2377 11058 - - (1.08) (1.13) HP 735 1286 5872 12640 32034 99 MHz (2.0) (2.1) (1.26) (1.06) IBM RS6000/580 976 4758 8891 - (2.6) (2.6) (1.79) DecAXP 3000/800 912 4296 6900 22582 (2.8) (2.9) (2.3) (1.50) IBM RS6000/590 555 2337 4327 14110 (4.6) (5.3) (3.7) (2.4) Cray YMP 392 1520 1832 7069 (6.6) (8.2) (8.7) (4.8) Keywords : HF Optimization %mem=4000000 #P RHF/6-31G* OPT SCF=DIRECT TEST POP=NONE HF Frequencies %mem=4000000 #P RHF/6-31G* FREQ GUESS=READ GEOM=CHECK SCF=DIRECT POP=NONE MP2 Optimization %mem=8000000 #P RMP2=(FULL,DIRECT,MAXDISK=60000000)/6-31G* OPT=READFC SCF=DIRECT POP=NONE GUESS=READ GEOM=CHECK TEST MP4 Energy %mem=8000000 #P RMP4SDTQ/6-31G* GUESS=READ GEOM=CHECK POP=NONE TEST The full inputs are available upon request. __________________________________________________________________________ From: jmuilu@joyke7.joensuu.fi (Juha Muilu) Here is short summary of g92 execution times (test job 178) I have compiled from several sources.. Computer Proc MHz Nproc LP 178 G92 Version Mflops min -------------------------------------------------------------------- SGI Indigo/32Mb R4000 50/100 1 16 111 RevC.3 SGI Indigo/32Mb R4400 75/150 1 24 80 RevC.3 IBM RS6000 590/256MB Power2 66 1 132 20 RevE IBM RS6000 590/256MB Power2 66 1 132 17 RevG3 IBM RS6000 380/32MB Power2 57 1 50 45 RevE IBM RS6000 370 Power 62 1 26 57 IBM RS6000 550 Power 42 1 26 61 IBM RS6000 540 Power 30 1 19 83 IBM RS6000 32H/16MB Power 25 1 12 134 RevB DEC 3000 AXP 800/Unix Alpha 200 1 44 RevE.2 DEC 3000 300 Alpha 150 1 144 DEC 3000 500X Alpha 200 1 59 DEC 3000 AXP 400/VMS Alpha 133 1 26 90 RevG.2 Cray X-MP EA/432 117 1 66 17 CRAY C90 8/256 ~250 1 4.25 RevC.3 CRAY C90 8/256(incore) ~250 1 1.5 RevC.3 CRAY YMP EL 34 1 39 Convex C3840 37 1 39 Convex C3840 37 2 39 Nproc) Number of processors used. LP ) Linpack DP (100x100). 178) Test 178 from g92 test suite. Elapsed wall clock time in minutes. (Should be close to CPU+system time, when Nproc = 1) Number of basis functions: 300 SCF iterations: 8 Input stream: %mem=2000000 #P RHF/6-31G** scf=direct test pop=npa prop=fit Gaussian 92 Test Job 178: TATB rhf/6-31g**//hf/6-31g** Energy should be -1006.2213391 .... c Best Regards, Juha Muilu Department of Chemistry,University of Joensuu,P.O. Box 111 80101 Joensuu,FINLAND Email:Juha.Muilu@joensuu.fi (NeXT mail ok) Phone:358-73-1513312,Fax:358-73-1513390 ------------------------------------------------------------------------ From Mckelvey@Kodak.COM Several addenda for recent benchmarkings of Gaussian G3 and TEST0178 SGI/R8000 16 Min (By Roberto Gomperts at SGI) IBM 590/pwr2 17 Min (Kodak) IBM 390/pwr2 41 Min (Kodak; Same executable images as for 590/pwr2) 90 Mhz Pentium 600 Min (Kodak; Micronics mb with 512K cache and 32MB memory) Regards -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 Thank you all who found the time to read or even reply. Regards, Peeter -- Peeter Burk, Ph.D. Jakobi 2, EE2400 Tartu, Estonia Institute of Chemical Physics Phone (372-7) 441-453 Tartu University Fax (372-7) 441-453 Estonia E-mail peeter@chem.ut.ee From grzesb@asp.biogeo.uw.edu.pl Fri Nov 25 05:22:13 1994 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id EAA18199; Fri, 25 Nov 1994 04:25:38 -0500 Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA22132; Fri, 25 Nov 94 10:29:13 +0100 Date: Fri, 25 Nov 94 10:29:13 +0100 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9411250929.AA22132@asp.biogeo.uw.edu.pl> To: CHEMISTRY@ccl.net Subject: SUMMARY: Mulliken Population Analysis and Basis Sets Dear CCLNet, Last Monday I asked a question on how much charges from Mulliken population analysis can depend upon basis set, especially using diffusive functions. Thanks to all you who replied. I think that every suggestion is worth reading. Thank a lot Yours sincerely Grzegorz Bakalarski Warsaw University Poland _________________________________________________________ This is summary of replies I've got until Friday morning: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Original query: Dear Netters, Maybe this is a very naive question, but .... I'd like to ask you Dear Quantum Chemists, how much charges from Mulliken population analysis can depend upon basis set ? Particular problem is that I and coworkers have calculated Mulliken charges using different programs using different basis sets e.g.. gaussian 6-31G** basis set ( in GAUSSIAN) and double numerical with polarization basis set (DNP in DMol). And of course we've got different Mulliken charges. (As we've expected and as it is well know that Mulliken charges depend on basis sets). But we've noticed that for some atoms differences are quite large. For example when a methyl group is bound to nitrogen atom changes are about 0.7-0.8 e (6-31G** : -0.188 [MP2] ;-0.193 [B3-LYP] and DNP: -0.962 [LDF]; -0.786 [NLDF]). I'd like to ask especially about comparison between DNP and gaussian + diffusive basis sets, because as I know numerical basis sets are "more diffusive" than gaussian ones (they have "good tails"). I'd like to add that we've also calculated ESP charges and they are O.K. (differences less than 0.1 e), that means that electron density is calculated correctly. Any comments, references and hints would be nice. Thanks in advance for anyone who replies. If I get any useful information I'll summarize to the NET. Best wishes and have a nice week. Grzegorz Bakalarski Dept. of Biophys. UW & Interdisciplinary Centre for Modelling (ICM) Warsaw University Poland e-mail: grzesb@asp.biogeo.uw.edu.pl $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ R E P L I E S $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ There is a very nice review related to this topic: Reviews in Computational Chemistry, Vol. 5, Libkowitz, Boyd (Eds.). I can't remember by whom it was, right now, but if you look in the book you will surely find it. The author favors Loevdin populations over Mulliken populations and discusses the "atoms in molecules" approach by Baader. The shortcomings of each method are discussed! Hope this helps, 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 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: "Erin Duffy" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Hi - You might want to take a look at the following: (1) Carlson, HA; Nguyen, TB; Orozco, M.; Jorgensen, WL. "Accuracy of Free Energies of Hydration for Organic Molecules from 6-31G(d)-Derived Partial Charges." J. Comput. Chem. (1993) v.14, 1240-1249. (2) Wiberg, KB; Rablen, PR. "Comparison of Atomic Charges Derived via Different Procedures." J. Comput. Chem. (1993) v.14, 1504-1518. Ciao - Erin erin@lorentz.csb.yale.edu (Erin Duffy) &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: "FOUNTAIN, KEN" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The answer is "Lots!" In Gaussian computations fluctuations abound, depending on the level of theory. In fact the entire area of populations seems to be murky. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: "Robert K. Szilagyi" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dear Dr. Grzegorz Bakalarski, we found some systematical changes in Mulliken Population analysis while varying basis sets. Our system contains transition metal and we are utilizing effective core potentials. The magnitude of the charges was changed, the inductive effects, electrophility, etc. remain the same. I will send you a note if this article will accepted by the publisher. Sincerely Yours, Rob Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: young@slater.cem.msu.edu (Dave Young) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Hello, There was a question about basis set dependence of the mulliken population analysis. Generally, the answer is that there is a basis set dependence and it is often very large. The arbitrary 50-50 split of overlap populations makes some sense for minimal basis sets and covalent compounds. For ionic compounds, 50-50 split should be suspect immediately. With diffuse basis sets, the diffuse functions may be so far from the nucleus they are centered on that they are describing the other nuclei more than the one they are centered on. Somewhat better results are obtained with the Reid & Weinhold natural orbital analysis. Probably the least basis set dependent results come from the electrostatic analysis in which atomic charges are determined by a least squares fit to the electrostatic potential. Hope this helps. Dave Young young@slater.cem.msu.edu youngdc@msucem &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: evaldera@amadeus.ivic.ve (Elmer Valderrama) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Hi, Just in case you haven't check this source, I. Levine in "Quantum Chemistry" (1991) wrote: `One should not put too much reliance on numbers calculated by population analysis. Mulliken's assignment of half the overlap population to each basis function is arbitrary and sometimes leads to unphysical results (see Mulliken & Ermler, Diatomic Molecules, (1977) p. 36-38, 88-89). Moreover, a small change in basis set can produce a large change in the calculated net charges. For example, net charges on each H atom in CH4, NH3, and H2O calculated by the STO-3G and 3-21G basis set are (Hehre et al. Ab Initio Molecular Orbital Theory (1986), Sec. 6.6.2) CH4 NH3 H2O ----------------------- STO-3G 0.06 0.16 0.18 3-21G 0.20 0.28 0.36 Comparison of values calculated with the same basis set correctly shows increasing charge on each H atom as the electronegativity increases from C to N to O, but comparison of the values calculated with different basis sets could erroneously lead one to say that the C-H bond in CH4 is more polar than the O-H bond in H2O." "Many other methods have been proposed to assign charges to atoms in molecules. See P. Polizer et al. Theor.Chim. Acta 38 101 (1975); J. Cioslowsky, J.Am.Chem.Soc 111 8333 (1989); Hehre, Sec. 6.6.2)" -What follows is that you could carry out a detailed analysis of the results from both DNP and n-nnG type calcns but since no unitary transformation connect these wave functions, all would be reduced to just a basis-set-dependent effect. Elmer &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From: inoue@greencross.co.jp (Yoshihisa Inoue) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dear Dr. Grzegorz Bakalarski, I think Mulliken population analysis is historically important, but actually sometimes perplexes researchers. As you know, the charges are used for molecular dynamics or monte carlo calculations. Then, I think they should have physicochemical meaning. Following two reports might be useful for you. TI Comparison of Atomic Derived via Different Procedures AU Kenneth B. Wiberg and Paul R. Rablen SO J.Comp.Chem.,14(12), 1504-1518 (1993) TI Electron Density Distribution Analysis for Nitromethane, Nitromethide, and Nitramide AU James P. Ritchie SO J.Am.Chem.Soc.,107,1829-1837 (1985) The former examined the charges with physicochemical properties. You seems to use DMol, so I suggest to use Hirshfeld charges. We also reported that Hirshfeld charges are very good at WATOC'93 at Toyohashi, Japan. Dr.Ritchie made Rhosys and it can handle gaussian basis functions. According to the JACS report, he provided the program. And Drs.Wiberg and Rablen wrote that the Hirshfeld charges were obtained using programs written at Yale. Hope this help. ____/ ___/ ___/ Yoshihisa INOUE (^_^) the Green Cross Corp. / / / 2-25-1 Shodai-Ohtani,Hirakata,Osaka 573 JAPAN / _ / / / tel: +81-720-56-9328 / / / / fax: +81-720-68-9597 _____/ _____/_____/ E-mail: inoue@greencross.co.jp $$$$$$$$$$$$$$$$$$$$$$$$$$$$ T H E E N D $$$$$$$$$$$$$$$$$$$$$$$$$$$$$ From Jeffrey.Gosper@brunel.ac.uk Fri Nov 25 09:14:40 1994 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA19928; Fri, 25 Nov 1994 09:10:51 -0500 Received: from chem-pc-13.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <08274-0@monge.brunel.ac.uk>; Fri, 25 Nov 1994 12:59:50 +0000 Date: Fri, 25 Nov 1994 14:09:52 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:MO packages. To: "S. Kent Worsnop" cc: chemistry@ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > I need to be able to draw accurate MO diagrams/energy level > diagrams however lack the software to do this. So I would like to > ask if anyone knows of some shareware products that do these diagrams > and also where I can find them. Please respond by e-mail. > I don't know of any shareware, we use ChemX (which is expensive) if you come across any shareware material I would be more than interested as I have written a chemical viewer which gets its data from QM output. From deakz@cdk-cgx.hu Fri Nov 25 11:14:44 1994 Received: from sztaki.hu for deakz@cdk-cgx.hu by www.ccl.net (8.6.9/930601.1506) id KAA20743; Fri, 25 Nov 1994 10:39:03 -0500 Received: by sztaki.hu with UUCP (5.67a8/SZTAKI-3.13) id no02104; Fri, 25 Nov 1994 16:33:18 +0100 Received: by cdk-cgx.hu (UUPC/extended 1.11x1.4e); Fri, 25 Nov 94 16:18:22 +0100 Date: Fri, 25 Nov 94 16:18:20 +0100 From: deakz@cdk-cgx.hu (Zoltan Deak) Message-Id: <2ed6003e.hu021da@cdk-cgx.hu> To: chemistry@ccl.net Cc: zdeak@goliat.eik.bme.hu Comment: EMIL 1.61: COMGENEX kutatasi-fejlesztesi KFT peldanya Subject: Chemical software predicting pKa and logP under windows X-Charset: US X-Char-Esc: 0 Dear Reader, We are pleased to let you know that our programs: pKalc 3.0 predicting the D I S S O C I A T I O N C O N S T A N T (pKa) and PrologP 5.0 predicting the P A R T I T I O N C O E F F I C I E N T (logP) are available for Windows platform from NOW ON. If you are interested in details, we would be pleased to answer you. Free demo version can be accessed via anonymous ftp on www.ccl.net in: /pub/chemistry/software/MS-WINDOWS/pKa_logP_logD-demo directory. There are 2 files there: pka_logp_demo.txt contains detailed information pka_logp_demo.zip demo software These can also be gotten via gopher (www.ccl.net port 73), WWW: http://www.ccl.net/chemistry.html OR retrieved via CCL e-mail interface to archives. Yours sincerely, Zoltan Deak CompuDrug Chemistry Ltd. Marketing Department e-mail: deakz@cdk-cgx.hu From underhil@hp.rmc.ca Fri Nov 25 13:14:44 1994 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.6.9/930601.1506) id NAA21789; Fri, 25 Nov 1994 13:05:53 -0500 Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP id AA28320 (5.67b/IDA-1.5 for ); Fri, 25 Nov 1994 13:00:33 -0500 Date: Fri, 25 Nov 1994 13:00:33 -0500 Message-Id: <199411251800.AA28320@sv2.rmc.ca> X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: Solubility reference I'm looking for a good review article on calculating a material's solubility in a variety of solvents. I'm particularly interested in the solubility of polymers. Does anyone have a favourite they can recommend? Thanks Ross Underhill From states@ibc.wustl.edu Fri Nov 25 19:10:08 1994 Received: from wugate.wustl.edu for states@ibc.wustl.edu by www.ccl.net (8.6.9/930601.1506) id TAA24618; Fri, 25 Nov 1994 19:10:08 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA16622; Fri, 25 Nov 1994 18:10:04 -0600 Received: by ibc.WUStL.EDU (8.6.9/SMI-SVR4) id SAA24067; Fri, 25 Nov 1994 18:10:03 -0600 Date: Fri, 25 Nov 1994 18:10:03 -0600 From: states@ibc.wustl.edu (David J. States) Message-Id: <199411260010.SAA24067@ibc.WUStL.EDU> To: chemistry@ccl.net, tds26@cas.org Subject: Re: CCL:Introducing CXF - WWW browser X-Sun-Charset: US-ASCII As those of you who have tried to explore the CXF definitions will immediately discover, they are quite complex. To ease the process of learning them, I implemented a WWW hypertext interface to the definitions that others might find useful. Take a look at: http://ibc.wustl.edu/standards/ The biological sequence asn.1 definitions from the National Center for Biotechnology Information are also available on the same menu. David States Institute for Biomedical Computing / Washington University in St. Louis From mrigank@imtech.ernet.in Fri Nov 25 19:14:46 1994 Received: from sangam for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id SAA24503; Fri, 25 Nov 1994 18:40:01 -0500 Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id PAA17947 for chemistry@ccl.net; Thu, 24 Nov 1994 15:06:03 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA04954; Thu, 24 Nov 94 14:55:14+050 Message-Id: <9411240955.AA04954@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Wed, 23 Nov 94 21:35:19 +0530 Date: Wed, 23 Nov 94 21:35:19 +0530 From: Mrigank To: chemistry@ccl.net Subject: Protein Structure analysis:Summary I posted a querry on programs for prtein conformatoinal analysis. i recievd lots of reply. I am summarizing the replies here. Original replioes can be asked if some one wants. Mrigank ___ One: Protein Expert (for MAC with math coprocessor) can do some nice analysis of protein structure, including comparisons of structures digested into a database of sequence, distance and angle relationships. You can search for motifs. Volume comparisons of proteins is also quite complete. A demo is available at www.camsci.com --- Two: For protein structure analysis, you could try the pkb by Steve Bryant. The program itself is free, but it requires an Splus license to run (see below). The pkb is freely available via anonymous ftp over internet. They are present on ncbi.nlm.nih.gov, in the compressed tar archive pub/pkb/pkb.tar.Z. The files in this directory are a distribution of the PKB program system. This is PKB version 3.0. It comes from: Steve Bryant National Center for Biotechnology Information National Library of Medicine, National Institutes of Health 8600 Rockville Pike Bethesda, Maryland 20894 Phone: (301) 476-2475 Email: bryant@ncbi.nlm.nih.gov PKB is provided to you free of charge as an academic exchange. Please fell free to use and/or modify the programs as you see fit. I cannot guarantee you support, but will try to answer questions. Please acknowledge use of PKB in scientific publications, if appropriate. Please do not redistribute PKB without permission, nor incorporate it into any commercial product. Let me know what you do with PKB, or what you'd like to do but can't! Comments and questions from users have helped me improve the system, and I'd like to continue the process! Steve Bryant, 5/6/93 ----- Three: in order to obtain P-curve, you better contact one of the authors, Prof. Heinz Sklenar at the Max-Delbrueck-Centre for Molecular Medicine, Robert-Roessle-Str. 10, 13122 Berlin, United States of Germany. His Telephone is likely to be +49-9406-2561, e-mail sklenar@orion.rz.mdc-berlin.de . ---- Four: I am not so sure whether the program PROCHECK would help you or not. Perhap, you can try to look it. The program is available from ftp 128.40.46.11 /pub/procheck/tar3_0_1 or /pub/procheck/source3_0_1. ----- All those who reponded: Stefan Unger dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) "Konrad, IRBM Chemistry, +39-6-91093606" h0159cap@rz.hu-berlin.de (Frank Eisenmenger) thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) toni@athe.wustl.edu (Toni Kazic) Thanks a million to all of you Mrigank ---- Mrigank \/Phone +91 172 49057 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in Sector 39A, \/FAX: +91 172 40958, +91 172 28032 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