From CFCIJZER@rulgl.LeidenUniv.nl Fri Jul 30 10:56:35 1993 Date: Fri, 30 Jul 1993 09:56:35 +0100 (MET) From: CFCIJZER@rulgl.LeidenUniv.nl Subject: MOPAC and ion-ion interaction To: chemistry@ccl.net Message-Id: <01H15E1M80N68WW139@rulgl.LeidenUniv.nl> Dear netters, we're studying the interaction between i) methanol and ammonia (CH3OH and NH3) and ii) methanolate and ammonium (CH3O- and NH4+) using MOPAC with AM1. It is possible to calculate the heats of formation of all individual partners in these interactions. It is also possible to calculate the interaction between the uncharged species (CH3OH and NH3), yielding stabilization through hydrogen bonding. This is all in line with Dewar et al., JACS 107 (1985) 3902-3909. However, the calculation of the interaction between the charged species (CH3O- and NH4+) causes problems. I realize that such a charge-charge interaction in vacuo is not very likely, but I would nevertheless be very much interested. Since the total complex is uncharged the keyword CHARGE is (probably) of no use, but in that case MOPAC is willing to do anything but keeping the charges intact. Who can help us out? Ad IJzerman cfcijzer@rulgl.LeidenUniv.nl From vkitzing@sunny.mpimf-heidelberg.mpg.de Fri Jul 30 12:33:02 1993 From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Message-Id: <9307300833.AA01310@sunny.mpimf-Heidelberg.mpg.de> Subject: Re: Solvation Methods - looking for recent articles To: balbes@osiris.rti.org (Lisa Balbes) Date: Fri, 30 Jul 1993 10:33:02 +0200 (MET DST) > > > Hi. I am looking for information on current methods of treating > solvent in modelling studies. The most recent review I have been able > to find is "Solvation Effects", Richards, King and Reynolds, > Protein Engineering, _2(5)_, 319-327 (1989). W.F. von Gunsteren & H.J.C. Berendsen (1990) Angew. Chem., Int. Ed. Engl. 29, 922 R. A. Friedman and B. Honig (1992) "The Electrostatic Contribution to DNA Base-STacking Interactions" Biopol 32, 145-159 ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.mpimf-heidelberg.mpg.de From chp1aa@surrey.ac.uk Fri Jul 30 06:15:55 1993 From: Mr Andrew D Allen Message-Id: <9307300936.AA13937@central.surrey.ac.uk> Subject: Solvation To: chemistry@ccl.net Date: Fri, 30 Jul 93 10:36:02 BST Dear Lisa, I have a summary of Solvation, which I put out in the Net some months back. I have tried mailing to "balbes@osiris.rti.org@ and to lmb@rtifs2.rti.org" and both fail to get through. If you want a copy of the file then you can pick it up on our local ftp server. ftp 131.227.110.2 login as anonymous give mail ID as password filename is Solv.txt Hope this is of use. Andy From JKONG@ac.dal.ca Fri Jul 30 06:50:04 1993 Date: Fri, 30 Jul 1993 09:50:04 -0300 From: JKONG@ac.dal.ca Subject: Re: Size-limit of file systems To: chemistry@ccl.net Message-Id: <01H15DQ6TAME00APO5@AC.DAL.CA> From: IN%"sdudis%bmsuem11.bitnet@utcc.utoronto.ca" 30-JUL-1993 08:53:30.68 To: IN%"JKONG@ac.dal.ca" CC: Subj: RE: ? limit of file systems on IBM RISC/6000 Dear netters, The following is a reply to my question about the size-limit of file systems. Those who are limited might be interested in it. Jing Kong Reply... Your file limitation problem is one we have been trying to overcome for some time now, and for exactly the same reason. If you want a SYSTEM larger than2 GB, that is possible with disk-striping, as we have currently conencted over 23 GB into one system (literally a tmp space with over 23 GB in the one ~directory~). However, if you wish to write INDIVIDUAL files larger than 2 GB, that indeed is a limit of the 32 bit machine (it's an addressing problem - with one bit taken for the sign). We have talked to every vendor I am aware of (IBM, Sun, SGI, HP + others - and don't feel slighted if I leave you out) -- NONE can deliver, to the best of my knowledge (and we looked for it specifically) a capability of > 2 GB files. A Cray can as it is based on a 64 bit word AND the operating knows it| The good knews (in a vaporware sense) is that most of the workstations coming out now ARE based on 64 bit words. BUT - the operating systems don't know it yet. It is a classic case of the hardware leading the software (i.e. systemware?). Several vendors, who shall remain nameless, have promised the capability of > 2 GB files ~in the next release of the operating system~ (almost the same words exactly from several vendors|). If this is enough of an issue for many of us, it might be useful to keep letting the vendors know. The initial responses I got were ~not enough people are interested in it to make it a hot issue~. Obviously, those who need it need to make it an issue. It won't take too many lost sales to vendors who get it first to bring everyone else along. Hope that helps. Doug Dudis Polymer Branch Wright-Patterson AFB, OH Disclaimer: The opinions expressed above are solely my own and in no way reflect those of my employer. This statement is not believed to harm the atmospheric ozone in any way (no kidding folks - in the government we are now having to put such a silly disclaimer with all purchase requests - the current one being a charge for journal pages|) From markm@portal.vpharm.com Fri Jul 30 04:16:51 1993 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9307301316.AA16567@portal.vpharm.com> Subject: Drug deformation energy in the active site? To: chemistry@ccl.net Date: Fri, 30 Jul 1993 09:16:51 -0500 (EDT) Hey gang. I'm looking for references to different points of view about how much "deformation energy" can be tolerated upon the binding of an inhibitor to an enzyme. Yes, I know there is no absolute answer to this question. I'm looking for attempts to quantify how much deformation energy is actually seen in various cases, and what sort of theoretical limits might be postulated. I'll summarize results. / Mark From breitkopf@chemie.uni-halle.d400.de Fri Jul 30 17:47:04 1993 Date: Fri, 30 Jul 1993 15:47:04 +0200 From: breitkopf@chemie.uni-halle.d400.de Message-Id: <930730154704*/S=breitkopf/OU=chemie/PRMD=UNI-HALLE/ADMD=D400/C=DE/@MHS> To: CHEMISTRY@ccl.net Subject: GROMOS Hi, I have a few questions concerning with the GROMOS-package. I'll try to calculate 1,2-diols. Since there are only some examples for the input of amino acids I have problems to create input files and parameter files for not predefined molecules. Who has experience with such input files for a version without graphic interface? Thanks. From o.casher@ic.ac.uk Fri Jul 30 10:41:42 1993 From: o.casher@ic.ac.uk Message-Id: <9307301354.AA11746@cscmgb.cc.ic.ac.uk> Subject: Explorer Chemistry Summary To: CHEMISTRY@ccl.net Date: Fri, 30 Jul 93 14:54:41 bst Aloha again! I didn't expect such a large number replies to my posting yesterday regarding my Explorer chemistry modules being displayed at SIGGRAPH (stand #2240). Soooo... for all of you who requested, I've put together a brief summary of most of the modules that I have developed or am developing presently. Their means of distribution is being finalized. You can contact me if you want to know more. For those of you who will be attending SIGGRAPH, have fun! - Omer Summary of the Explorer Chemistry Modules developed at the Department of Chemistry, Imperial College, London. READERS: *EyeMopac: Inputs a standard Mopac output or archive file (versions 5, 6 or 7) and outputs an Explorer molecular data type output. The user specifies whether the connectivity is determined from: 1) a covalent radius table that the user can readily modify. 2) a bond order calculation. *EyeMopacVib: Inputs a standard Mopac output FORCE file and outputs sequences of molecular data to simulate molecular vibrations for the chosen Eigenvalue. In all other respects it is identical to EyeMopac. *EyeMopacRxn: Inputs a standard Mopac output file that has additional reaction coordinates and outputs sequences of molecular data to simulate molecular movement and reactions. *EyeMopacESP: Inputs a Mopac ESP output file and outputs a uniform grid lattice suitable for issosurfacing. *EyeG92: Inputs standard Gaussian 92 files and outputs molecular data for the chosen iteration. A sequence of iterations can be simulated to show how the calculation is progressing. *EyeG92Vib: Similar to EyeMopacVib. *EyeG92ESP: Similar to EyeMopacESP. *EyeBackbone: Inputs a Brookhaven Date Bank protein and extracts the geometry and residue information of the backbone atoms and then assembles it into a molecular data type. *EyeCrystal: Inputs a CSSR or Cambridge crystal data file and outputs molecular data. The Explorer MopacView module was modified here to allow the MO's and electron densities to register with the above modules. A Gaussian version is under development. LATTICE MANIPULATORS: *EyeESP: Inputs the point charge information of an Explorer molecular data type and calculates the ESP lattice. Although more flexible than the ESP readers mentioned above - the user can vary the grid spacing and bounding box in the module - it does not give as fine a detail. *EyeMonteCarlo: Inputs an Explorer lattice and calculates the volume of a selected piece using the MonteCarlo integration. GEOMETRY MODULES: *EyeBalls: Inputs an Explorer molecular data type and outputs geometry information for atoms (spheres), and for single, double, and triple bonds (cylinders or lines). The user can vary the sphere radius, bond width, and the number of polygons. *EyeRibbons: Inputs the molecular data from EyeBackbone and outputs protein ribbons (threads or sheets) that run in line with the peptide plane. Currently under development is an open-ended molecular renderer/editor (IChem) and related modules using the Iris Inventor object oriented toolkit. It will run in Explorer. P.S. I do recall reading a post here on molecular animation for video. Just to add in my two bits, we don't have the required equipment for video. However if you have and would like to make some videos with Explorer, email me. I'll try to set up the first few respondents with the necessary modules and maps. -- Omer Casher (P.G.) o.casher@ic.ac.uk Molecular Modelling Laboratory Or +44 071-589-5111 (x3988) (fibre optic chemistry) "For every fool there is an even Imperial College, London SW7 2AZ bigger fool that will worship him." From rob@retina.chem.psu.edu Fri Jul 30 06:42:30 1993 Date: Fri, 30 Jul 93 10:42:30 -0400 From: rob@retina.chem.psu.edu (Rob Stanton) Message-Id: <9307301442.AA08164@retina.chem.psu.edu> To: CHEMISTRY@ccl.net Subject: Ti parameters/basis sets Recently I have been trying to find in the literature what has been done to date with quantum mechanical calculations involving Ti. Any references would be greatly appreciated. In particular references to previously used HF or DF basis sets (pseudopotentials would be a bonus) or even published semiemperical parameters would be helpful. In general, I would really like to hear about the present state of the art in Ti calculations. Robert V. Stanton ____________________________________________________________________________ /\ /\ ^^ ^^ Robert V. Stanton \ ^^ ^^ tel 814-863-7591 /\ /\ email rob@retina.chem.psu.edu /\ /--\/__\ /\ ^^ 404 Chandlee Lab /--\/ \ \/--\ Penn State University / / \ / \ Univ. Park, PA 16803 / / \/ \ USA Go Climb a Mountain!! _____________________________________________________________________________ From DAVID%UCONNVM.BITNET@phem3.acs.ohio-state.edu Fri Jul 30 06:02:22 1993 Date: Fri, 30 Jul 1993 11:02:22 -0500 (EST) From: Carl David Subject: GenBank? To: chemistry@ccl.net Message-Id: <01H15GN3VDC68WXTJ4@phem3.acs.ohio-state.edu> I need to access a primary protein structure which has been deposited in the "GenBank/EMBL Data Bank" with accession number ... Can someone help me locate this site (and presuambly its e-mail address) so that I can access this data? Thanks. Carl David From schwegle@chemsun.chem.umn.edu Fri Jul 30 06:06:17 1993 From: "Eric Schwegler" Message-Id: <9307301606.AA02707@chemsun.chem.umn.edu> Subject: Line widths To: chemistry@ccl.net Date: Fri, 30 Jul 93 11:06:17 CDT Hello, Is there anyone out there who is interested in the different computational models used to estimate Raman collision broadening widths? I am particularly interested in how one might model the rotational line widths of a homonuclear diatomic dissolved in water. Any references or suggestions are welcomed. ---------------------------------------------------------- Eric Schwegler schwegle@chemsun.chem.umn.edu Department of Chemistry tel: (612)626-1829 University of Minnesota fax: (612)626-7541 ---------------------------------------------------------- From quelch@hartree.chem.wfu.edu Fri Jul 30 10:37:03 1993 From: quelch@hartree.chem.wfu.edu (Geoffrey E. Quelch) Message-Id: <9307301837.AA10255@hartree.chem.wfu.edu.chem.wfu.edu> Subject: File system limits To: CHEMISTRY@ccl.net Date: Fri, 30 Jul 93 14:37:03 EDT Organization: Chemistry Department Just to add another data point to this discussion. According to Sun, the 2Gb file system limit is due to a UNIX definition (the 31 bit address space). Sun have a program suite called "Online: Disksuite" which can do a whole bunch of things, including creating >2Gb partitions. Some sales talk: PRODUCT DESCRIPTION ------------------- Online: DiskSuite provides three key capabilities: 1) Disk mirroring for data availability 2) Data striping across disks and controllers for higher I/O throughput 3) Support for creation and extension of UNIX(R) file systems larger than 2 GB. Limitations in the previous release have been removed. The number of configured "meta-devices" can be increased simply by changing a configuration file and rebooting. Sizes of stripes and concatenations can be changed dynamically at runtime. Cost is reported to be ~$1k (US). I believe that the main problems are with newfs and fsck, which have this 31-bit address limitation built in. Hope this is of interest. -- Geoffrey E. Quelch | Internet quelch@hartree.chem.wfu.edu Department of Chemistry | quelch@hbar.phy.wfu.edu Wake Forest University | Voice: +1 (919) 759 4717 Winston-Salem, NC 27109 | Fax: +1 (919) 759 4656 From jaeric@mtcamm.monsanto.com Fri Jul 30 08:49:38 1993 From: Jon A. Erickson Message-Id: <9307301849.AA05497@mtcamm.monsanto.com> Subject: Re: Ti parameters/basis sets To: chemistry@ccl.net (OSU Comp. Chem. List) Date: Fri, 30 Jul 93 13:49:38 CDT > Recently I have been trying to find in the literature what has been done to > date with quantum mechanical calculations involving Ti. Any references would > be greatly appreciated. In particular references to previously used HF or DF > basis sets (pseudopotentials would be a bonus) or even published semiemperical > parameters would be helpful. In general, I would really like to hear about the > present state of the art in Ti calculations. > > Robert V. Stanton I believe INDO1 has parameters for Ti (in Argus, for example). -- ################################################################ # Jon Erickson e-mail: jaeric@mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. FAX: (314) 694-1080 # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ From bishop@lisboa.ks.uiuc.edu Fri Jul 30 11:09:27 1993 From: Tom Connor Bishop Message-Id: <9307302109.AA07334@lisboa.ks.uiuc.edu> Date: Fri, 30 Jul 93 16:09:27 -0500 To: chemistry@ccl.net Subject: DNA-protein interactions? hello netters, i'd appreciate any refs that you might supply to reviews on protein-DNA interactions, particularly molecular dynamics, crystal, and NMR studies and also refs to theoretical models that have been proposed. i'll of course compile a list for the network. thanks in advance, tom