From edvard@atf1.fagmed.uit.no Tue Jul 27 11:35:26 1993 Date: Tue, 27 Jul 93 10:35:26 +0100 From: edvard@atf1.fagmed.uit.no (Oyvind Edvardsen Computer Graphics Lab. IMB Univ. Tromsoe) Message-Id: <9307270935.AA01648@atf1.fagmed.uit.no> To: cchem@atf1.fagmed.uit.no Subject: Helix axis Peter C. Kahn have published an article on "Defining the axis of a helix" in Computers & Chemistry, vol. 13(3):185. It is stated that the procedure is more rapid than non-linear least squares regression. Does anybody out there know if this method, or other 'helix axis' methods are available on the net as source code? Thanks! -oed. From msrag@csv.warwick.ac.uk Tue Jul 27 15:07:36 1993 Date: Tue, 27 Jul 1993 14:07:36 +0100 From: Dr D Buttar Message-Id: <24302.199307271307@violet.csv.warwick.ac.uk> To: chemistry@ccl.net Subject: RRKM calculations Does anyone know of any public domain software that is available for performming rrkmm calculations. An ftp site for such software would be very useful. Cheers, David Buttar. From berkley@wubs.wustl.edu Tue Jul 27 04:35:11 1993 Date: Tue, 27 Jul 93 09:35:11 -0500 From: berkley@wubs.wustl.edu (Berkley Shands) Message-Id: <9307271435.AA04231@wubs.wustl.edu> To: chemistry@ccl.net Subject: More benchmarks CPU benchmarking for current architectures July, 1993 Software is an analytic ring closure method on an eight membered ring (cylooctane) from the Sybyl library. No log files were written to minimize overhead. "System" is measured system overhead. "Confs" are stericly allowed conformers. "Scan" is the rotation scan increment if an integer otherwise it is the maximum swept arc in Angstroms for each rotatable bond. "Forks" is the number of fork() system calls. * CycloOctane Relative Orientation 07/26/93 No log files, no output * wubs2 DEC Alpha AXP 3000/300 Ringsearch ~96 confs/second cpu Confs Elapsed CPU System Scan 1919681 19665 19609.398 2.367 0.01 240858 2524 2517.233 0.400 0.02 131134 1388 1379.050 1.400 1 71572 740 737.300 0.100 0.03 30295 326 322.767 0.333 0.04 16409 175 174.767 0.033 2 15717 170 169.600 0.033 0.05 9015 97 96.450 0.017 0.06 5645 62 61.567 0.033 0.07 4894 52 51.600 0.017 3 3799 42 41.800 0.033 0.08 2711 28 28.333 0.033 0.09 2044 22 22.050 0.033 4 1973 22 21.850 0.017 0.1 1075 11 11.533 0.033 5 282 3 3.033 0.017 0.2 79 1 0.917 0.017 0.3 44 1 0.467 0.017 0.4 20 1 0.233 0.000 0.5 cmdi6a IBM rs/6000-560 Ringsearch ~57 confs/second cpu Confs Elapsed CPU System Scan 131134 2388 2230.090 0.000 1 16409 333 290.240 0.000 2 4894 102 86.750 0.000 3 2044 42 36.330 0.000 4 1075 22 18.460 0.000 5 Multisearch (multi-threaded ringsearch) cs2 sun sparc-1000 2 cpus ~80 confs/second cpu ~120 confs/sec elapsed ~0.2 seconds/fork overhead Elapsed User System Ratio Forks Scan 849 1556.190 78.270 1.833 360 1 143 205.940 40.210 1.440 180 2 54 66.480 22.940 1.231 120 3 30 30.140 16.640 1.005 90 4 20 17.040 12.770 0.852 72 5 wuecl sun Sparc2-690 2/4 cpus ~28 confs/second cpu ~50 confs/second elapsed ~1.0 seconds/fork Elapsed User System Ratio Forks Scan 2433 4385.167 424.333 1.802 360 1 380 569.817 177.000 1.500 180 2 142 174.733 105.483 1.231 120 3 74 76.367 71.067 1.032 90 4 50 39.350 59.883 0.787 72 5 wucmd sgi 4d/380 4/8 cpus ~35 confs/second cpu ~130 confs/second elapsed ~0.1 seconds/fork overhead Elapsed User System Ratio Forks Scan 913 3463.170 97.690 3.793 360 1 125 469.310 22.510 3.754 180 2 38 139.510 11.250 3.671 120 3 18 59.730 9.100 3.318 90 4 10 29.590 6.980 2.959 72 5 wucmd sgi 4d/380 8/8 cpus ~37 confs/second cpu ~280 confs/second elapsed ~0.1 seconds/fork overhead Elapsed User System Ratio Forks Scan 798 5986.950 49.360 7.502 431 0.02 247 1863.640 27.020 7.545 287 0.03 111 808.920 19.480 7.288 216 0.04 56 403.120 14.880 7.199 173 0.05 Berkley Shands berkley@wubs.wustl.edu From carlos@extreme.bio.cornell.edu Tue Jul 27 06:23:00 1993 Date: Tue, 27 Jul 93 10:23:00 -0400 From: carlos@extreme.bio.cornell.edu (Carlos Faerman) Message-Id: <9307271423.AA27394@extreme.bio.cornell.edu> To: chemistry@ccl.net Subject: summary of answers concerning calculation of pKa's. This is what I got on pK calculation of small molecules, not including a bunch of calls for the summary. Thanks for all contributions. -regards J. Symersky ------------------------------------------------------------------------------- Try SPARC, which will soon be (is now?) available via the internet from the University of Georgia. Contact Butch Carriera at UGA or Sam Karickoff at EPA's labs in Athens. Sorry, I don't have phone numbers, I only know these guys from meetings and beer . . . CJC P.S. It could be Carreira . . . Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 ------------------------------------------------------------------------------- You might want to look at the recent paper by Tunon, Silla and Pascual-Ahir, JACS 115, 2226 (1993), then trace back through the references to earlier work, especially by Tomasi and co-workers (e.g. Tunon, Silla and Tomasi, J. Phys. Chem. 96, 9043, 1992). This model uses a model that inserts solutes in a continuum solvent, using ab initio quantum calculations for the solute portion. The basic method goes back (at least) to Miertus, Scrocco &Tomassi, Chem. Phys. 55: 117 (1981). Several groups (including ours) are working on similar models that use density functional quantum mechanics; I don't know that any papers on this method have actually appeared yet. A good reference to some preliminary work along these lines, with classical models, is Lim, Bashford & Karplus, J. Phys. Chem. 95: 5610 (1991). There are lots of semi-empirical quantum mechanical approaches, some of which are covered in the first reference cited above. Remember that 1 pK unit is about 1.4 kcal/mol at room temperature, so any method for calculating pK's that is going to be generally useful has to be pretty accurate, getting both gas-phase proton affinities and solvation free energies to within about 1% accuracy. It may be necessary to go beyond continuum descriptions of solvation to obtain reliable results. Bill Jorgensen's group has long been active in the area of computing solvation interactions via Monte Carlo calculations; also check out the work of Arieh Warshel, e.g. in his book "Computer Modelling of Chemical Reactions in Enzymes and Solutions" (Wiley, 1991). An interesting recent example of this sort of approach (including both quantum-mechanical and solvation aspects) is in Gao & Xia, Science, 258: 631 (1992). This has (necessarily) been a pretty subjective selection of things I have seen, and emphasizes recent papers; you will have to trace back to earlier literature from that. I'd be interested in seeing what other replies you get. I don't know of any really good recent review on this subject, but that doesn't mean there hasn't been one. ...good luck ...dave case ===================================================================== David A. Case | internet: case@scripps.edu Dept. of Molecular Biology | bitnet: case%scripps.edu@sdsc The Scripps Research Institute | fax: 619-554-6717 10666 N. Torrey Pines Rd. | phone: 619-554-9768 La Jolla CA 92037 USA | ===================================================================== ------------------------------------------------------------------------------- As far as I can remember, Bill Jorgenson at Yale had published a paper on the theoretical calculation of pka's a few years ago in JACS. Cant tell you the exact year and ref. But you could check against his name. -S. Srivastava ------------------------------------------------------------------------------- Bill Jorgensen has written an empirical fragment pKa estimator which is incorporated in the synthesis program Cameo. I think the original publication of the method only worked for DMSO, but the version in Cameo also works for water. I found that the values among diverse structures are not as accurate as the publication suggests, but along a series I was working with it rank ordered the compounds pretty well. At the opposite extreme of computational resources, Jorgensen has also used free energy perturbation simulations with a thermodynamic cycle involving free energy of solvation to get aqueous acidities from gas phase values. I am very interrested to see your summary. Cheers, -Eric Martin ------------------------------------------------------------------------------- There is a public domain program that calculates pKs using electrostatic energies available. Please contact Dr. Don Bashford via e-mail at: bashford@riscsm.scripps.edu He will be able to give you a hand. mssommer ------------------------------------------------------------------------------- From kb7@tower.york.ac.uk Tue Jul 27 15:30:16 1993 Date: Tue, 27 Jul 1993 14:30:16 +0100 (BST) From: K Bryson Subject: Calculating charges for charged molecules. To: CHEMISTRY@ccl.net Message-Id: Dear Computational Chemists, I've calculated the partial charges for various polyamines ( putrescine, spermine, etc ) using MOPAC 6.0 and B.H. Besler's ESP routine. I get roughly the following charges : + Primary aminium NH_3 / N = -0.40 H = +0.36 + Secondary aminium NH_2 / \ N = +0.01 H = +0.27 I've noticed that I.S. Haworth et al ( Proc. Roy. Soc. Lond.(1991) V.244 p107-116) got very different charges using AMPAC AM1 method for spermine and a home-constructed fitting similar to Besler's : Primary : N = +0.04 H = +0.26 Secondary : N = +0.08 H = +0.26 ( All to 2 dec. places ) Now the secondary aminium is agreeable, but my primary aminium is quite different. So who is using the correct charges ? Are any of these reasonable charges ? Does anyone know of a database which might provide good ab-initio charges for polyamines ? Relating to this K.M. Merz ( J. Comp. Chem. (1992) V.13 No.6 p. 749 ) mentions that he has research in progress determining the accuracy of semiempirical methods on charged species, can anyone provide citations for this type of work ? As a final note I would be interested in any citations of computational work done on polyamines, I noticed a similar posting a year ago but cannot locate the person who posted it. I will repost a summary of the responses I receive, but also feel it would be worth-while getting an open discussion on the feasibility of partial charge calculations for charged species. Many thanks, Kevin. ----------~~~~~~------~~~~~~~~~~---------------~~~~~----------~~~~~-- K.Bryson email: kb7@tower.york.ac.uk Biophysics Group Tel : +44 904 430000 Extn. 2236 Physics Department Fax : +44 904 432214 University of York Heslington "Molecular modelling of DNA and its YORK, UK interaction with small molecules." YO1 5DD -------------------~~~~~-------------~~~~--------~~~~--------~~~~~--- From tom@sgih.roc.wayne.edu Tue Jul 27 11:07:35 1993 Message-Id: <9307271909.AA04910@sgih.roc.wayne.edu> Date: Tue, 27 Jul 1993 15:07:35 -0400 To: chemistry@ccl.net From: tom@sgih.roc.wayne.edu (Tom Wiese) Subject: Unwinding DNA ? Hello all, I would like to get in contact with someone that has experience with or has ideas on how to unwind a molecular model of DNA such that a simulation of intercalating agents interacting with DNA can be made. We have SYBYL and have tried various things like the DOCK command but have produced only very odd and deformed final DNA structures. If there is a program that runs on SGI, and somehow unwinds the DNA (enlarges the major and minor groves while opening up the space between base stacking) and still maintains the inter-strand H-Bonds I would love to get my hands on it or at least hear about it! Any comments might be useful. Thanks in advance, Tom Wiese ################################################## Tom Wiese Department of Biochemistry Wayne State University School of Medicine 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-5605 FAX: (313) 577-2765 email: tom@sgih.roc.wayne.edu ################################################## From adams@nmr1.oscs.montana.edu Tue Jul 27 09:25:55 1993 Date: Tue, 27 Jul 93 15:25:55 -0600 From: adams@nmr1.oscs.montana.edu (Earl Adams) Message-Id: <9307272125.AA07729@nmr1.oscs.montana.edu> To: CHEMISTRY@ccl.net Subject: distance dependent dielectric hello, I have been trying to use a distance dependent dielectric for MD calculations of a peptide+metal system in water using the Discover package. I have gone through some papers and I really haven't found any definite rules on how to use it properly. I was wondering if any out there might have some suggestions or good references on how to get a handle on the distance dependent dielectric. thank you earle adams -- ------------------------------------------------ Earle Adams adams@hydrogen.oscs.montana.edu From DWARKNTH@ACFcluster.NYU.EDU Tue Jul 27 13:26:58 1993 Date: Tue, 27 Jul 1993 18:26:58 -0500 (EST) From: DWARKNTH@ACFcluster.NYU.EDU Subject: RE:Unwinding DNA? To: chemistry@ccl.net Message-Id: <01H11OZI38VMV7QQYS@ACFcluster.NYU.EDU> In response to Tom question about unwinding the DNA: Try to increase the dihedral angle between either C5'-O5'-P-O3' OR C3'-O3'-P-O5' in the DNA backbone. By doing this , the DNA looks unwound and you can also see a difference in the major and the minor groove.We have seen this happen when we minimize modified DNA with AMBER. Good Luck. _____________________________________________________________________________ Sulatha Dwarakanath Dept. Of Biology New York University NY 10003. E-Mail:dwarknth@acfcluster.nyu.edu. _____________________________________________________________________________