From lingran@EROS.CCC.Uni-Erlangen.DE Mon Oct 9 04:54:02 1995 Received: from enar.organik.uni-erlangen.de for lingran@EROS.CCC.Uni-Erlangen.DE by www.ccl.net (8.6.10/950822.1) id EAA04535; Mon, 9 Oct 1995 04:45:56 -0400 Received: by enar.organik.uni-erlangen.de id AA18113 for CHEMISTRY@www.ccl.net (5.65c/IDA-1.4.4/bs-02); Mon, 9 Oct 1995 09:45:25 +0100 Date: Mon, 9 Oct 1995 09:45:25 +0100 From: Lingran Chen Message-Id: <199510090845.AA18113@enar.organik.uni-erlangen.de> To: CHEMISTRY@www.ccl.net Subject: on HOSE codes > A nomenclature, "Hose codes", confused me when I read a paper, CSEARCH: A > Computer Program for Identification of Organic Compounds and Fully Automated > Assignment of Carbon-13 Nuclear Magnetic Resonance Spectra (H. Kalchhauser et > al., J. Chem. Inf. Comput. Sci., 1985, 25, 103). Could someone give me a clue > about it? > > Thank yuo! > > Jianguo Yu The HOSE code is a substructure code developed by W. Bremser. Please see W. Bremser: HOSE-A Novel Substructure Code, Anal. Chim. Acta 1978, 103, 355-365. -Lingran Chen ====================================================================== ...................................................................... Lingran Chen, Ph.D. COMPUTER UNIVERSIT NAGELSBAC Computer-Chemistry-Center C | E Y S H University of Erlangen-Nuernberg H R T Naegelsbach Strasse 25 E L R D-91052 Erlangen M A 2 Germany I N 5 N Tel : +49-(0)9131-85 65 78 S G G D E Fax : +49-(0)9131-85 65 66 T R E R 9 G E-Mail: RY-CENTE N-NUERNBE 1052ERLAN Lingran.Chen@EROS.CCC.Uni-Erlangen.de ...................................................................... ====================================================================== From fekete@chi3.bc.edu Mon Oct 9 08:24:05 1995 Received: from chi3.bc.edu for fekete@chi3.bc.edu by www.ccl.net (8.6.10/950822.1) id IAA06852; Mon, 9 Oct 1995 08:21:04 -0400 Received: by chi3.bc.edu (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA11885; Mon, 9 Oct 95 11:17:58 -0400 Date: Mon, 9 Oct 1995 11:17:58 -0400 (EDT) From: "Zoli Fekete, keeper of hungarian-faq" Reply-To: fekete@bc.edu To: Jan Labanowski Cc: chemistry@www.ccl.net Subject: Re: CCL:Stupid adds In-Reply-To: <199510090238.WAA14387@krakow.ccl.net> Message-Id: X-Url: http://hix.mit.edu/hungarian-faq/ Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I should point out that the 'From:' line is totally useless in fighting malicious email (for the magazine spam is not merely stupid - it's a product of an infamous net abuse, who could not have any hope to generate profit). It is al too easily forgeable, as it clearly was in out case. However, the situation is not nearly as hopeless as Jan described! A close look at the header information reveals that the CCL listserv does authenticate the sender's host: >Received: from [198.70.48.43] (actually pm1-44.ixc.net) > by nd.edu with SMTP (PP); Sat, 07 Oct 1995 22:57:44 -0500 (and various other dial-in machines at ixc.net in similar instances) - that is the domain that ought to be filtered out, not the bogus sender address. Also notice that email-bombing the perpetrator, even if targeted right (which was not the case for the pieces of advice surfacing on CCL), is not an effective way to fight this plague. The culprits are prepared (using throwaway accounts and such), and usually don't need to use their email box anyways. But the mass of email meant to flood them has to travel thru the network, wasting resources and quite possibly bringing down the often innocent host system perhaps together with ones connecting to it! On the other hand they may have installed some system that just throws the incoming mail away, so the revenge would not have any effect at all. So the recourse one must use is turning to the system administrators (eg. postmaster@ixc.net and the postmasters of the email drops employed for this scheme, ie. postmaster@grfn.org). If they do not respond then the site next in the link should be contacted - responsible administrators are ready to stem such abuses exploiting their system. -- Zoli fekete@bc.edu, keeper of <'finger hungarian-faq-pointer@hix.mit.edu'> "For my assured failures and derelictions, I ask pardon beforehand of my betters and my equals in my calling." - Rudyard Kipling From harris@MIT.EDU Mon Oct 9 09:09:05 1995 Received: from MIT.EDU for harris@MIT.EDU by www.ccl.net (8.6.10/950822.1) id JAA08305; Mon, 9 Oct 1995 09:02:32 -0400 Received: from LIQUID2-SUN.MIT.EDU by MIT.EDU with SMTP id AA02005; Mon, 9 Oct 95 09:02:00 EDT Received: by liquid2-sun.MIT.EDU (5.0/4.7) id AA04097; Mon, 9 Oct 1995 09:02:32 -0400 Message-Id: <9510091302.AA04097@liquid2-sun.MIT.EDU> To: CHEMISTRY@www.ccl.net Subject: Punishing net abusers Date: Mon, 09 Oct 1995 09:02:32 EDT From: "Jonathan G. Harris, Dept. of Chem Eng, MIT" Content-Length: 743 A suggestion on how to fight stupid ads: Pretend you are interested and get them to waste a considerable amount of time on you (if you can do so at little or no effort on your part). This minimizes their profit and maxmimizes their expenses. When I used to receive phone calls from penny stock brokers I recognized as frauds from various media sources I would do things like say "I'm very interested, send literature" "call me back at XXX in California tomorrow", and "Please hold for just a minute while I deal with my boss and then we will talk..." ---Jonathan Jonathan G. Harris Associate Professor Department of Chemical Engineering, MIT Rm 66-450 25 Ames Street, Cambridge, MA 02139 harris@athena.mit.edu (617)253-5273 Fax 252-1651 From tmoc@gibbs.oit.unc.edu Mon Oct 9 09:14:51 1995 Received: from gibbs.oit.unc.edu for tmoc@gibbs.oit.unc.edu by www.ccl.net (8.6.10/950822.1) id JAA08417; Mon, 9 Oct 1995 09:06:55 -0400 Received: from localhost by gibbs.oit.unc.edu (8.6.4.3/10.1) id JAA04615; Mon, 9 Oct 1995 09:06:55 -0400 Date: Mon, 9 Oct 1995 09:06:54 -0400 From: "Thomas M O'Connell" To: chemistry@www.ccl.net Subject: RE:Vanishing atoms in Charmm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Alex, Is it possible that some solvent waters are flying away during the dynamics? Have you tried running the simulation with the quartic droplet potential or using stochastic boundaries? If you think these might help I can give you further details on setup. Cheers, tom ------------------------------------------------------------ Original question: I must thank you all for the help that you have supplied so far. I have a very strange one for you now. I have a quenched dynamics run going on Charmm 22.2, using 15A TIP3 sphere to dissolve methyl- glycoside. I used ABNR to minimise to tolgrd 0.001 and then used a fairly standard quenched dynamics run. The snag is that after 300 steps then program says that some of the atoms have undefined co-ordinates. Has anyone every come across this before. ------------------------------------------ ********************************************** Thomas M. O'Connell, Ph.D. Laboratory for Molecular Modeling School of Pharmacy, CB #7360 University of North Carolina Chapel Hill, NC 27599-7360 phone (919) 966-7821 fax (919) 966-6919 e-mail tmoc@gibbs.unc.edu From owner-chemistry@ccl.net Mon Oct 9 10:39:09 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA10753; Mon, 9 Oct 1995 10:37:20 -0400 Received: from grizzly.ucla.edu for BGoodin@UNEX.UCLA.EDU by bedrock.ccl.net (8.6.10/950822.1) id KAA21512; Mon, 9 Oct 1995 10:37:19 -0400 Received: from UNEXGW.UCLA.EDU ([128.97.218.2]) by grizzly.ucla.edu (8.6.9/8.6.9) with SMTP id HAA39072; Mon, 9 Oct 1995 07:07:19 -0700 Received: by UNEXGW.UCLA.EDU with Microsoft Mail id <30792C7D@UNEXGW.UCLA.EDU>; Mon, 09 Oct 95 07:06:53 PDT From: "Goodin, Bill" To: List-Biotechnology , List-Biotechnology business , "'List-Computational chem2'" , List-Chemistry modeling , "'List-Chemical engineering'" , List-Computational chemistry , List-Chemistry & Industry To: List-Macromolecular engineerin , List-Polymers , List-Polymer chemistry Cc: "Goodin, Bill" Subject: UCLA short course on "Computer-Aided Molecular Design" Date: Sun, 08 Oct 95 17:12:00 PDT Message-ID: <30792C7D@UNEXGW.UCLA.EDU> Encoding: 55 TEXT X-Mailer: Microsoft Mail V3.0 On February 12-15, 1996, UCLA Extension will present the short course, "Computer-Aided Molecular Design", on the UCLA campus in Los Angeles. The instructors are Richard Judson, PhD, Sandia National Laboratories; Michael Colvin, PhD, Sandia National Laboratories; and Tony Hopfinger, PhD, University of Illinois at Chicago. This course provides a broad introduction to computer-aided molecular design. It describes how computational methods can be appropriately applied to real-world problems in the pharmaceutical, biotechnology and chemical industries. A variety of methods are discussed, ranging from statistical methods based on experimental data to high level ab initio quantum chemical calculations. The methods to be introduced include molecular dynamics, quantum chemistry, statistical methods such as QSAR (Quantitative Structure Activity Relationships), and diffusion and compartment models for drug delivery. Sections of the course also introduce homology-based protein modeling and general purpose optimization methods used across a range of computational chemistry methods. The course combines descriptions of methods with applications to specific areas, including predictions of physical properties of molecules (solubilities, conformations, pKa, diffusion coefficients, etc.), predictions of binding properties of drugs (binding geometries and energetics), and statistical prediction of various properties from experimental data. Each method is illustrated with a case study, and the material in the lectures are reinforced through hands-on computer laboratory sessions. The course is designed to benefit: o Professionals in the pharmaceutical, biotechnology or chemical industry who are evaluating the usefulness of molecular modeling o Professionals moving into the area of modeling o Modelers who are expert in one field but who wish to broaden their expertise. Major benefits from the course include: o How computer modeling can be used for the design of molecules o How to choose the appropriate modeling method for specific problems o How to apply standard molecular modeling tools o How to assess the accuracy of predictions made by computer models. The course fee is $1395, which includes extensive course materials. For additional information and a complete course description, please contact Marcus Hennessy at: (310) 825-1047 (310) 206-2815 fax mhenness@unex.ucla.edu From asnegb01@asnmail.asc.edu Mon Oct 9 11:09:08 1995 Received: from asnmail.asc.edu for asnegb01@asnmail.asc.edu by www.ccl.net (8.6.10/950822.1) id KAA11316; Mon, 9 Oct 1995 10:57:41 -0400 Received: by asnmail.asc.edu (AIX 3.2/UCB 5.64/4.03) id AA20130; Mon, 9 Oct 1995 10:00:37 -0500 Date: Mon, 9 Oct 1995 10:00:35 -0500 (CDT) From: "Eric G. Bradford" To: CHEMISTRY@www.ccl.net Subject: Gauss-Hermite Quadrature Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am attempting to port an ab initio code from RISC to CRAY. There is a problem which occurs within a routine used to generate the integrals - Gauss-Hermite quadrature minimum-point formula. The routine name is STVINT and is the same found in other ab initio codes. The problem is the calculation of xint, yint, and zint at the end of the routine. The lines in question follow: xint = xint+dum*px yint = yint+dum*py zint = zint+dum*pz dum is a value set in a data statement and px, py, pz are calculated during the routine. On a RISC machine (IBM, HP), the above lines calculate dum*px as the negative value of xint. Therefore xint = xint + (-xint) = 0.0 The same is true for yint and zint. However, on the CRAY, dum*px is calculated as a value close to the negative of xint. Therefore xint = xint + dum*px = ~1.0E-17 Has anyone had similar difficulties porting codes from RISC to CRAY. Are there methods or tricks I can use to correct this "problem" on the CRAY. The present situation does not cause the code to abort but it does cause the incorrect number of integrals to be generated on the CRAY. Eric G. Bradford, Ph.D. Nichols Research Corporation Alabama Supercomputer Network email: asnegb01@asnmail.asc.edu phone: (205) 934-3893 fax: (205) 934-9245 From asnegb01@asnmail.asc.edu Mon Oct 9 11:24:12 1995 Received: from asnmail.asc.edu for asnegb01@asnmail.asc.edu by www.ccl.net (8.6.10/950822.1) id LAA11670; Mon, 9 Oct 1995 11:18:48 -0400 Received: by asnmail.asc.edu (AIX 3.2/UCB 5.64/4.03) id AA08134; Mon, 9 Oct 1995 10:21:45 -0500 Date: Mon, 9 Oct 1995 10:21:44 -0500 (CDT) From: "Eric G. Bradford" To: CHEMISTRY@www.ccl.net Subject: Gauss-Hermite Quadrature Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am attempting to port an ab initio code from RISC to CRAY. There is a problem which occurs within a routine used to generate the integrals - Gauss-Hermite quadrature minimum-point formula. The routine name is STVINT and is the same found in other ab initio codes. The problem is the calculation of xint, yint, and zint at the end of the routine. The lines in question follow: xint = xint+dum*px yint = yint+dum*py zint = zint+dum*pz dum is a value set in a data statement and px, py, pz are calculated during the routine. On a RISC machine (IBM, HP), the above lines calculate dum*px as the negative value of xint. Therefore xint = xint + (-xint) = 0.0 The same is true for yint and zint. However, on the CRAY, dum*px is calculated as a value close to the negative of xint. Therefore xint = xint + dum*px = ~1.0E-17 Has anyone had similar difficulties porting codes from RISC to CRAY. Are there methods or tricks I can use to correct this "problem" on the CRAY. The present situation does not cause the code to abort but it does cause the incorrect number of integrals to be generated on the CRAY. Eric G. Bradford, Ph.D. Nichols Research Corporation Alabama Supercomputer Network email: asnegb01@asnmail.asc.edu phone: (205) 934-3893 fax: (205) 934-9245 ----- End of the message ----- From ioan@servidor.unam.mx Mon Oct 9 12:09:09 1995 Received: from servidor.dgsca.unam.mx for ioan@servidor.unam.mx by www.ccl.net (8.6.10/950822.1) id MAA12590; Mon, 9 Oct 1995 12:02:06 -0400 Received: by servidor.dgsca.unam.mx (5.0/SMI-SVR4) id AA27041; Mon, 9 Oct 1995 10:03:39 +0600 Date: Mon, 9 Oct 1995 10:03:38 -0600 (CST) From: Silaghi Dumitrescu Ioan-IQ X-Sender: ioan@servidor To: chemistry@www.ccl.net Subject: G94 performance on a sun (SPARCstation 20) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 365 Dear netters, I am addressing to those of you who have installed G94 on a sun (SPARCstation 20) of 32M, 50 Mhz and 1Gb disk space. Can you send me please the CPU times needed for running test000, 1,2 and test178? Ioan. Dr. Ioan Silaghi-Dumitrescu Universidad Nacional Autonoma de Mexico Instituto de Quimica 04510 Mexico D.F. e-mail : ioan@servidor.unam.mx From owner-chemistry@ccl.net Mon Oct 9 19:09:15 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA22562; Mon, 9 Oct 1995 18:58:40 -0400 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by bedrock.ccl.net (8.6.10/950822.1) id SAA26486; Mon, 9 Oct 1995 18:58:34 -0400 Message-Id: <199510092258.SAA26486@bedrock.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA15640; Mon, 9 Oct 95 16:56:47 -0500 From: Ramon Garduno Subject: (?) SETOR To: chemistry@ccl.net (POST MSG's) Date: Mon, 9 Oct 95 16:56:46 CDT Mailer: Elm [revision: 70.85] Dear fellow netters: Does any one of you have an idea as to the whereabouts of SETOR (a hardware 3D solid model builder for macromolecules) by Stepehn Evans from the University of British Columbia, Canada?. Thanks a 10^6! Cheers, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From raman@bioc01.uthscsa.edu Mon Oct 9 23:10:31 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id XAA29234; Mon, 9 Oct 1995 23:05:29 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 9 Oct 1995 21:35:39 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA02961; Mon, 9 Oct 95 21:34:21 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9510100234.AA02961@bioc01.uthscsa.edu> Subject: Re: CCL:(?) SETOR To: ramon@ce.ifisicam.unam.mx (Ramon Garduno) Date: Mon, 9 Oct 1995 21:34:20 -0500 (CDT) Cc: chemistry@www.ccl.net In-Reply-To: <199510092258.SAA26486@bedrock.ccl.net> from "Ramon Garduno" at Oct 9, 95 04:56:46 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2045 Ramon: > Does any one of you have an idea as to the whereabouts of SETOR (a hardware > 3D solid model builder for macromolecules) by Stepehn Evans from the > University of British Columbia, Canada?. You can reach Stephen Evans at: elmo@nrcbsa.bio.nrc.ca He will be happy to supply you with the object code for the SGI. Source is not distributed at the present. A package similar to SETOR called PREPI is also available from a colleague of mine, Suhail Islam (ICRF, UK). Both Setor and PREPI are provided free-of-charge for academia. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/