From omar@crs4.it Thu Apr 29 11:44:42 1993 Message-Id: <9304290744.AA20755@malena.crs4.it> To: "System Manager, and VAX Gopher" Subject: Re: Molecular Visualization. Date: Thu, 29 Apr 1993 09:44:42 +0200 From: "Omar G. Stradella" Your message dated: Wed, 28 Apr 1993 17:37:22 EDT >Hello all. > >Not to continue a thread beyond it's time, but I have been looking for a >package to allow the visualization of molecular orbitals and electron >densities, either on a PC or workstation. I found a reference in the >literature to a program called _Interactive MOPLOT_, which contains the >routines MOPLOT, PLOTDEN, SCHUSS, and EXTREM, and was published by >P. Sherwood and P.J. MacDougall in 1989. No further references, such as >where were provided. > >Does anybody have any details on this program, such as who to contact about >obtaining it, or whether there are any licensing details? Thank you. > > -Fred > farnold@wotan.duch.udel.edu I don't know much about Interactive MOPLOT, but the name of the subroutines (particularly SCHUSS and EXTREM) and the name of one of the authors (MacDougall) suggests that it is a program based on the programs produced by the group of Richard F.W. Bader et al at the Dept. of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1. For sure, EXTREM is a program used to locate critical points in the electronic density (and likely also in the laplacian). Omar. -- **************************************************************************** * Dr. Omar G. Stradella - Omar.Stradella@crs4.it * * CRS4 - Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna * * - Centre for Advanced Studies, Research and Development in Sardinia * * -------------------------+----------------------------+----------------- * * Casella Postale 488 | Via Nazario Sauro, 10 | 39 13' 19" North * * 09100 Cagliari CA | 09123 Cagliari CA | 9 6' 17" East * * Italy | Italy | * * -------------------------+----------------------------+----------------- * * Phone: +39 70 27 96 415 FAX: +39 70 27 96 400 or +39 70 24 10 18 * **************************************************************************** From nobody@Kodak.COM Thu Apr 29 03:20:44 1993 Date: Thu, 29 Apr 93 07:20:44 EDT From: nobody@Kodak.COM (Adi Treasurywala) Message-Id: <9304291120.AA09074@bcc9.kodak.com> To: chemistry@ccl.net Subject: Pharmacophores from peptides Hi, I was wondering if someone out there has a collection of refs that document success in designing small molecule ligands from pharmacophores that have been developed from peptide ligands. The discussion comes up reasonably frequently and I would like to have FACTS. Clearly the efforts of Marshall et al comes to mind but I was wondering if there were any others. Please note its PEPTIDE based pharmacophores that I am specifically interested in not small molecule-based pharmacophores. I will be happy to summarize for the net if there is a substantial response. If your communication is to be kept private or annonymous please indicate that. Thanks Adi M Treasurywala,Sterling Winthrop Inc,1250 South collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com From scsupham@reading.ac.uk Thu Apr 29 10:14:54 1993 From: scsupham@reading.ac.uk Date: Thu, 29 Apr 93 14:54:01 BST Message-Id: <8516.9304291354@scsscsc3> To: chemistry@ccl.net Subject: CaChe/Textronix ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 9 Hi, Does anyone from CaChe read this board ? If so, can they email me please ? john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From CULMER@uoft02.utoledo.edu Thu Apr 29 04:44:55 1993 Date: Thu, 29 Apr 1993 09:44:55 -0500 (EST) From: "Chuck Ulmer, D.A.Smith Group" Subject: Gaussian problems... To: chemistry@ccl.net Message-Id: <01GXKURSDT76006AVR@UOFT02.UTOLEDO.EDU> Since Doug Fox is out of town until May 4th, the Gaussian Help Line is unavailable until then. So, I am asking for help from any Gaussian users out there. Correct me if I am wrong, but shouldn't I be able to use any file system, whether NFS mounted or not, as my scratch space? I have set the environment variable "GAUSS_SCRDIR" in the g90.login to point to an NFS mounted disk (exported from a DEC ALPHA running OSF/1) and Gaussian core dumps with the following error: ********************************************** Gaussian 90: Stardent-Unix-G90RevJ 4-Jun-1990 27-Apr-1993 ********************************************** %CHK=COMPLX1.chk lock-new-file: Invalid argument sh: 924 Illegal instruction - core dumped G90 is running on a Stardent/Kubota Titan 3000 and the ALPHA exports the filesystem with the root uid set equal to 0. I have no problems writing to the NFS mounted file system from either machine, only Gaussian seems to have the problems. I have also tried making Gaussian write to other NFS mounted disks which are exported from DECstation 3100's with the same error. Is there something that I have missed, a problem with Gaussian, or a problem with Digital's NFS? Thanks in advance, Chuck -- Charles W. Ulmer, II culmer@uoft02.utoledo.edu A&S System Manager root@stardent.chem.utoledo.edu D.A.Smith Group University of Toledo Toledo, OH, 43606 WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMIT THE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808) From kmoore@ncsc.org Thu Apr 29 07:08:37 1993 Date: Thu, 29 Apr 93 11:08:37 EDT From: Kevin Moore Message-Id: <9304291508.AA29366@duck.ncsc.org> To: chemistry@ccl.net Subject: direct vs. in-core calculations >Richard, > >I beg to differ with your numbers. Using N^4/4 one calculates: > ># functions memory >----------- ------ > 100 -> 25 MW > 200 -> 400 MW > 300 -> 2025 MW > >However, the Gaussian manual says, and my own experience support it, >that for closed shell RHF calculations memory scales as N^4/8 plus >some additional memory, say 500,000 words. (G92 User's Guide p.88.) >My own experience has been that the additional .5 MW is too small, >a more realistic number is 100N*N. Using this formula one calculates: > ># functions memory >----------- ------ > 100 -> 12.5 + 1 = 13.5 MW > 200 -> 200 + 4 = 204 MW > 300 -> 1012.5 + 9 = 1021.5 MW It has been a while since I have sat down and worked this out (so someone can correct me if I am wrong), but I believe the best approximation is: N^4/8 + N^3/4 + N^2/2 This means that the table would be: # functions memory ----------- ------ 100 -> 12.8 Mw 200 -> 202.0 Mw 300 -> 1019.3 Mw Generally, I use N^4/8 + N^3/4 and then add about 0.5 Mw onto the end. In gaussian, you can run the calculation with 'scf=incore' and if you have not given it enough memory, it will fail at the beginning of the scf. You can then look at the output file and see how much memory is needed (the error includes a line saying how many words are needed). Since it is at the beginning of the scf, the cpu time loss is minimal. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From kmoore@ncsc.org Thu Apr 29 07:22:34 1993 Date: Thu, 29 Apr 93 11:22:34 EDT From: Kevin Moore Message-Id: <9304291522.AA29633@duck.ncsc.org> To: chemistry@ccl.net Subject: direct vs. in-core calculations One other point that is worth making is that even if you are performing the calculation with the 5 pure d functions, gaussian is doing the integral calculation using the 6 cartesian d functions and then performing a transformation. The default number of d functions varies with the basis set, so 6-31G* uses the cartesian set by default while 6-311G* uses the pure set by default (has to do with how the basis set was originally generated). For a 6-311G** calculation on benzene, if you assume 5d, then you will come up with N=144 rather than N=150. This would put your projection at 54.5Mw rather than the actual 64.1Mw (a large difference). ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From BROUWER@SARA.NL Thu Apr 29 12:26:41 1993 Message-Id: <199304291547.AA24533@oscsunb.ccl.net> Date: Thu, 29 Apr 93 17:36:56 CET From: Fred Brouwer Subject: Free Energy calculations To: "comp.chem.list" A few years ago techniques to calculate Free Energies from MD simulations (umbrella sampling, thermodynamic integration, free energy perturbation,..) were the subject of many research papers. In recent times I have not seen such papers. Why ? Is it because : - I read the wrong journals - people found these techniques not useful enough - the techniques are commonly used, and as such hidden inside research papers ? I look forward to responses, especially from those who developed the methods and from people who actually use them. Fred Brouwer dr. A.M. Brouwer Laboratory of Organic Chemistry , University of Amsterdam Nieuwe Achtergracht 129 , 1018 WS AMSTERDAM , The Netherlands phone 31 20 5255491, fax 20 31 5255670 From slow@romulus.cray.com Thu Apr 29 11:03:15 1993 Date: Thu, 29 Apr 93 16:03:15 CDT From: slow@romulus.cray.com (David Slowinski {x65020 CF/HREB}) Message-Id: <9304292103.AA15902@romulus.cray.com> To: kmoore@ncsc.org Subject: Re: direct vs. in-core Gaussian calculations How much does running Gaussian-92 incore help performance? I am very interested in learning about G-92 users' experiences with real problems. I currently have a gigaword Cray YMP-M92 that can run Gaussian-92 problems up to 300 basis functions incore. In another week or so I expect have a system that can handle 350 basis functions. I would be happy to (attempt to) run your SCF or MP2 Gaussian-92 problems incore in return for the direct timings on your system. Thank you kindly, David Slowinski Cray Research Inc Chippewa Falls, WI slow@cray.com 715-726-5020 From raman@bioc01.uthscsa.edu Thu Apr 29 11:31:22 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9304292131.AA08643@bioc01.uthscsa.edu> Subject: Peptide - Pharmacophores! To: adit@kodak.com Date: Thu, 29 Apr 1993 16:31:22 -0500 (CDT) Other than the continuing work of Marshal, there were two important papers in the field of Peptido-mimetics as pharmacophores and they are" 1. Simon,R.J. et al., [1992] Proc. Natl. Acad. Sci. USA 89, 9367-9371 "Peptoids: A modular approach to drug discovery" 2. Fincham,C.I. et al., [1992] J. Med. Chem. 35,1472-1484 " Amide bond replacements Incorporated into CCK-B selective 'Dipeptoids' " THIS ARTICLE HAS AN EXCELLENT INTRODUCTION WITH REFERENCES TO RELATED WORK. Also, see: Kerr, J.M. et al., [1993] J.Am. Chem.Soc. 115, 2529-2531 "Encoded combinatorial Pptide Libraries Containing Non-natural Amino acids" Hope this helps! N.B. I am assuming that you were referring to Garland Marshal!? -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ******************************************************************************