From mayer@cric.chemres.hu Wed Oct 16 04:15:09 1996 Received: from cric.chemres.hu for mayer@cric.chemres.hu by www.ccl.net (8.8.0/950822.1) id EAA17197; Wed, 16 Oct 1996 04:12:46 -0400 (EDT) Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA15872; Wed, 16 Oct 1996 09:55:05 +0200 Date: Wed, 16 Oct 1996 09:55:05 +0200 From: mayer@cric.chemres.hu (Mayer Istvan) Message-Id: <9610160755.AA15872@cric.chemres.hu> To: MVKOSEVICH@ilt.kharkov.ua, Matthew.Harbowy@tjlus.sprint.com, RPONEC@icpf.cas.cz, S.Suhai@dkfz-heidelberg.de, asomogyi@aruba.ccit.arizona.edu, belen@pctc.chemie.uni-erlangen.de, chemistry@www.ccl.net, pongor@para.elte.hu, valiron@gag.observ-gr.fr Subject: Warning of a virus From: SARECZ Lajos (by way of mayer@cric.chemres.hu)) Subject: Virus (fwd) Status: RO >I have got the following message from a colleague: > > > Warning of a new virus!!!! > > ====================================================================== > > DO NOT DOWNLOAD ANY FILE NAMED PKZIP300 REGARDLESS OF EXTENSION. > > A NEW Trojan Horse Virus has emerged on the Internet with the name > PKZIP300.ZIP, so named as to give the impression that this file is a > new version of the PKZIP software used to "zip" compressed files. DO > NOT DOWNLOAD THIS FILE UNDER ANY CIRCUMSTANCES!! If you install or > expand the file, the virus WILL wipe your hard disk clean and affect > modems at 14.4 and higher. This is an extremely destructive virus and > there is NOT yet a way of cleaning this one up. > > PLEASE PASS THIS ON TO ANYONE YOU KNOW. > > > From peon@medchem.dfh.dk Wed Oct 16 05:15:18 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.0/950822.1) id EAA17262; Wed, 16 Oct 1996 04:33:41 -0400 (EDT) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id KAA00643; Wed, 16 Oct 1996 10:33:41 +0200 (METDST) Received: from [130.225.177.59] by medchem.dfh.dk via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA26301; Wed, 16 Oct 1996 09:54:56 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Wed, 16 Oct 1996 10:33:40 +0200 To: iguana@one.net (Ray Crawford) From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:ab initio bond minimizations Cc: CHEMISTRY@www.ccl.net Dear Ray, Your problem is in no way unique, it happens to everybody who try crystal structures in ab initio optimizations. There are a couple of ways you can do this. First, the largest errors are for bonds to hydrogen, you could simply set them manually at better positions before starting the calculation (C-H ca 1.08=C5, give C an idealized geometry like tetrahedron for sp3, X-H generally shorter than C-H, there are lit. values for most types). This is easiest if you can generate a Z-matrix for your X-ray structure. My favourite method is to bring the molecule into a molecular mechanics program, restrain all heavy atoms and let the program optimize the hydrogens. Alternatively, you may want to allow also the heavy atoms some movement, most MM programs can do some kind of "tethering" to allow small relaxations. The most expensive option would be to restrict movement of the heavy atoms in the ab initio program, and let it find optimum values for the hydrogen, before starting the full optimization. An added complication: there is no guarantee that the crystal geometry is a local minimum in vacuo, especially if you have systems with strong charges, but it should definitely have a low energy if you allow relaxation. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From dsmith@CTCnet.Net Wed Oct 16 10:15:11 1996 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.0/950822.1) id KAA18518; Wed, 16 Oct 1996 10:10:09 -0400 (EDT) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id JAA28540; Wed, 16 Oct 1996 09:12:51 -0400 Date: Wed, 16 Oct 1996 09:12:51 -0400 Message-Id: <199610161312.JAA28540@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: fair market value? I need to determine the fair market value of the following computer system. Please respond directly to me rather than to the CCL, as there is really no need to spend excessive bandwidth on this. Thanks. HP 720 CRX 2 x 420 MB hard disk drives 48 MB RAM external CD ROM drive HPUX version 10 operating system Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology. From cburkhart@goodyear.com Wed Oct 16 15:15:12 1996 Received: from goodyear.com for cburkhart@goodyear.com by www.ccl.net (8.8.0/950822.1) id OAA20102; Wed, 16 Oct 1996 14:30:33 -0400 (EDT) Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA02890; Wed, 16 Oct 96 14:30:04 EDT Received: from rds2721 by rdsrv2 (4.1/SMI-4.1) id AA16274; Wed, 16 Oct 96 14:30:03 EDT Sender: burkhart@goodyear.com Message-Id: <3265298B.41C6@goodyear.com> Date: Wed, 16 Oct 1996 14:29:31 -0400 From: Craig Burkhart Organization: Goodyear Research X-Mailer: Mozilla 2.02S (X11; I; IRIX64 6.2 IP28) Mime-Version: 1.0 To: Computational Chemistry List Subject: Hydrocarbon Forcefields Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I have been struggling for some time to find an appropriate molecular forcefield for Nose'-Hoover NpT dynamics calculations on long chain linear and branched alkanes/alkenes at liquid densities. My selection of "appropriateness" concerns the reproduction of 300K densities and heats of vaporization or cohesive energy densities. I have used the all-atom OPLS (1994), the exp-6 version of DREIDING-II, MM2, Rappe's UFF, Sybyl, Hagler's CFF-93 and the 92 version of CHARMM. I have also used Theodorou & Suter's (1985) hybrid forcefield. All of these well-known parameterizations do not compute the observed properties to the degree of accuracy I require. My queries to my net-aware colleagues: 1) Do you have experience with liquid density NpT MD simulations of branched hydrocarbons? 2) If so, can you point me in the direction of a forcefield which you have found appropriate for the calculation of liquid densities and delta-Hvap? Thanks in advance. I will gladly summarize all responses for the list. Craig -- ---------------------------------------------------------------------------- ** GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! *** ----------------------------------+----------------------------------------- Papernet: Craig W. Burkhart |"I believe in the Church of Baseball. I've Goodyear Research |tried all the major religions and most of 142 Goodyear Blvd. |the minor ones...but there's too much Akron, OH 44305 |guilt in religion--you see there's no Mouthnet: 330.796.3163 |guilt in baseball...The only church that Faxnet: .3304 |really feeds the soul, day in and day out, Internet: cburkhart@goodyear.com |is the Church of Baseball". --Annie Savoy ----------------------------------+----------------------------------------- !!! WAIT 'TIL NEXT YEAR !!! WAIT 'TIL NEXT YEAR !!! WAIT 'TIL NEXT YEAR !!! ---------------------------------------------------------------------------- From jesus@canarylab.chem.nyu.edu Wed Oct 16 18:15:14 1996 Received: from is.nyu.edu for jesus@canarylab.chem.nyu.edu by www.ccl.net (8.8.0/950822.1) id SAA21042; Wed, 16 Oct 1996 18:01:54 -0400 (EDT) Received: from CANARYLAB.CHEM.NYU.EDU by is.nyu.edu; (5.65v3.0/1.1.8.2/23Sep94-1121PM) id AA22321; Wed, 16 Oct 1996 18:01:48 -0400 Received: by canarylab.chem.nyu.edu (940406.SGI/931108.SGI.AUTO.ANONFTP) for @is.NYU.EDU:CHEMISTRY@www.ccl.net id AA19102; Wed, 16 Oct 96 18:15:03 -0400 From: jesus@canarylab.chem.nyu.edu (Jesus M. Castagnetto M.) Message-Id: <9610162215.AA19102@canarylab.chem.nyu.edu> Subject: CCL: A description of structure file formats? To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Wed, 16 Oct 1996 18:14:59 -0500 (EDT) Organization: New York University, Department of Chemistry X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I have searched the CCL archives and several other web search engines/sites, but I could not find that anybody has compiled a list of the currently available molecular structure file formats, along with their respective format description. I know about the PDB, XYZ, MacroModel and some other formats, but not many. By no means my search was exhaustive, so if someone knows of good pointers related to this I will appreciate your input. I will summarize to the list the info I receive. Greetings and TIA for the help/hints/ideas/pointers. ----- Jesus M. Castagnetto M. | "Organic Chemistry: The practice Dep.of Chemistry - New York University | of transmuting vile substances 4 Washington Pl, Room 514. NY 10003 | into publications" (The Last Word- jesus@canarylab.chem.nyu.edu | The Ultimate Scientific Dictionary) From alain.kessi@psi.ch Wed Oct 16 19:15:15 1996 Received: from psizi1.psi.ch for alain.kessi@psi.ch by www.ccl.net (8.8.0/950822.1) id SAA21167; Wed, 16 Oct 1996 18:55:08 -0400 (EDT) Received: from localhost by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA18409; Wed, 16 Oct 1996 14:06:38 +0200 Sender: kessi@psizi1.psi.ch Message-Id: <3264CFCE.2F1C@psi.ch> Date: Wed, 16 Oct 1996 14:06:38 +0200 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: Mayer Istvan Cc: MVKOSEVICH@ilt.kharkov.ua, Matthew.Harbowy@tjlus.sprint.com, RPONEC@icpf.cas.cz, S.Suhai@dkfz-heidelberg.de, asomogyi@aruba.ccit.arizona.edu, belen@pctc.chemie.uni-erlangen.de, chemistry@www.ccl.net, pongor@para.chem.elte.hu, valiron@gag.observ-gr.fr Subject: Re: CCL:Warning of a virus References: <9610160755.AA15872@cric.chemres.hu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mayer Istvan wrote: > > From: SARECZ Lajos > Subject: Virus (fwd) > Status: RO > > >I have got the following message from a colleague: > > > > > > Warning of a new virus!!!! >From http://www.kabi.si/si21/f-prot/bull-223.html the following explanation: -------------- I received a warning about a harmful program called PKZIP300. What should I do? Don't worry too much. PKZIP300 was a Trojan Horse program which claimed to be a new version of the popular compression/packing utility PKZIP. Actually the program tried to format the hard disk. This Trojan was reported in a couple of places during spring 1995. After that, it has not been seen anywhere. For some reason, there was a renewed warning scare about the PKZIP300 Trojan during spring 1996. However, although the PKZIP300 Trojan does exist, it is extremely unlikely for anybody to actually run into it. V2.04g is the latest official version of PKZIP. -------------- Hope this helps ... -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From hrusak@ims.ac.jp Wed Oct 16 21:15:16 1996 Received: from ims1.ims.ac.jp for hrusak@ims.ac.jp by www.ccl.net (8.8.0/950822.1) id VAA21706; Wed, 16 Oct 1996 21:03:43 -0400 (EDT) Received: from ikarus.ims.ac.jp by ims1.ims.ac.jp (8.6.8+2.4Wb2/TISN-1.3M/R2) id KAA08306; Thu, 17 Oct 1996 10:02:39 +0900 Received: by ikarus.ims.ac.jp with Microsoft Mail id <01BBBBAE.BFBA93C0@ikarus.ims.ac.jp>; Wed, 16 Oct 1996 22:09:49 +-900 Message-ID: <01BBBBAE.BFBA93C0@ikarus.ims.ac.jp> From: Jan Hrusak To: "'CHEMISTRY@www.ccl.net'" Subject: iodine Date: Wed, 16 Oct 1996 22:09:47 +-900 Return-Receipt-To: Encoding: 12 TEXT Dear Netters, I would like to investigate closer the spectroscopy of the I3(-). Looking up some databases I could not find much information about the previous experimental and theoretical work done on this species. I would acknowledge if you could provide me with references I may have missed in my search or any other information available. Thanx Jan Hrusak hrusak@ims.ac.jp From iguana@one.net Wed Oct 16 22:15:16 1996 Received: from one.net for iguana@one.net by www.ccl.net (8.8.0/950822.1) id VAA21822; Wed, 16 Oct 1996 21:47:36 -0400 (EDT) Received: from iguana (port-10-5.access.one.net [206.112.194.45]) by one.net (8.7.5/8.7.5) with SMTP id VAA14262; Wed, 16 Oct 1996 21:47:22 -0400 Date: Wed, 16 Oct 1996 21:47:22 -0400 Message-Id: <199610170147.VAA14262@one.net> X-Sender: iguana@mail.one.net X-Mailer: Windows Eudora Version 2.0.3 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: CHEMISTRY@www.ccl.net From: iguana@one.net (Ray Crawford) Subject: Summary: ab initio conformational comparisons to crystal structures Cc: laidig@pg.com, iguana@one.net All, A few days ago I posted a request for information on how to go about minimizing a crystal structure using ab initio methods in order to examine the energetics necessary to get the molecule of question into the crystal conformation. Attached are the responses I received. Many thanks to you= all. XXXXXXXXX ORIGINAL POSTING: Howdy all -- I have a rather unique problem. I have a structure which was resolved from an electron density map. I wanted to compare this structure to another but when I went to do so using ab initio methods, I found that the single point energy of this molecule was horrendously large and any attempts to do energetic geometry minimizations led to different structures (changed torsions and bond angles). Further investigation led me to the conclusion that the main problem is that the errors in bond lengths (as small as they were) were drowning out the effects which I wanted to see the energetic changes for (torsional and angular changes). I recently saw a paper about a topic similar to this (I think it was in the Journal of Computational Chemistry)... If anyone has any references to work in this area or any ideas about how I can go about comparing these structures, I would appreciate it if you passed it on... All information will be promptly summarized and resubmitted... Thanks, Ray Crawford "Absence of proof is not proof of absence..." iguana@one.net -Richard= Levine http://w3.one.net/~iguana The Lost World = =20 Micheal Crichton ########## The problem is that crystal structure mostly is not the structure which is minimal by energy. I recall the paper of Gilson et al. in Proteins a few years ago. They calculated energies in crystal and minimal states these were quite different :) Igor ------------------------------------------------ IGOR TSIGELNY Ph.D. University of California, San Diego itsigeln@ucsd.edu ############ Dear Ray, I just read your recent posting to CCL regarding electron density map vs. ab initio bond minimization. Now I don't know, which system this is, but could it be, that the experimental geometry, valid for the bulk, indeed does not represent an energy minimum of the molecule in vacuo. Of course, to decide this, one would have to look into the inter-molecular forces possibly present in the solid. Have you considered using a 3D code, atomistic or ab initio to clarify this aspect? One clue to the fact, that this maight indeed be the case should come from the experimental structure: are there any parameters that seem awkward or chemicaly unlikely, indicating a molecule under strain? Any obvious intermolecular forces (like hydrogen bridge bonds)? Cheers, Lutz Ackermann <^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^> < Dr. Lutz Ackermann > < Research Assistent > < The Royal Institution of Great Britain > < Davy-Faraday Research Laboratory > < 21 Albemarle Street > < London W1X 4BS > < UK > < > < phone: +44-171-409 2992 ext 424 > < FAX: +44-171-629 3569 > < e-mail: lutz@ri.ac.uk > < http://www.ri.ac.uk/DFRL/L.Ackermann > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv ######## Hi! This might seem a bit thick - but cannot you define your crystal structue as a zmatrix (get xmol to read it in - say pdb) then write it out as a gaussian zmatrix. Now using opt=3Dzmat , you can define your bonds as variables and everything else as constants. This should fix your system at a given conformation but optimise your bond lengths. I can suggest other ways - but that sounds aabout the most straight forward. Le t me know if I have completely missed the point! Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | -------------------------------------------------------------------=20 ########## Ray, We've seen similar (bond lengths incompatibility) problems, albeit mostly with MM and semiempirical calculations, in the context of a study we= published some time ago (Nicklaus, M.C., Wang, S., Driscoll, J.S., Milne, G.W.A.,=20 "Conformational Changes of Small Molecules Binding to Proteins", = =20 Bioorg.Med.Chem. 3(4), 411-428, 1995). These problems, and the way *we* solved them, are discussed briefly in this paper. We've also done some ab initio calculations---not reported there---where we saw the same effect of errors in bond lengths posing a problem for the exploration of torsional and angular changes. Hope this helps. Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ ######### Dear Ray, Your problem is in no way unique, it happens to everybody who try crystal structures in ab initio optimizations. There are a couple of ways you can do this. First, the largest errors are for bonds to hydrogen, you could simply set them manually at better positions before starting the calculation (C-H ca 1.08=C5, give C an idealized geometry like tetrahedron for sp3, X-H generally shorter than C-H, there are lit. values for most types). This is easiest if you can generate a Z-matrix for your X-ray structure. My favourite method is to bring the molecule into a molecular mechanics program, restrain all heavy atoms and let the program optimize the hydrogens. Alternatively, you may want to allow also the heavy atoms some movement, most MM programs can do some kind of "tethering" to allow small relaxations. The most expensive option would be to restrict movement of the heavy atoms in the ab initio program, and let it find optimum values for the hydrogen, before starting the full optimization. An added complication: there is no guarantee that the crystal geometry is a local minimum in vacuo, especially if you have systems with strong charges, but it should definitely have a low energy if you allow relaxation. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ ############ Thanks Again, Ray Crawford iguana@one.net