From haney@netcom.com Tue Nov 7 03:46:54 1995 Received: from netcom11.netcom.com for haney@netcom.com by www.ccl.net (8.6.10/950822.1) id DAA08934; Tue, 7 Nov 1995 03:36:14 -0500 Received: by netcom11.netcom.com (8.6.12/Netcom) id AAA11066; Tue, 7 Nov 1995 00:35:23 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199511070835.AAA11066@netcom11.netcom.com> Subject: CompChem Customization Services To: CHEMISTRY@www.ccl.net Date: Tue, 7 Nov 1995 00:35:23 -0800 (PST) Cc: haney@netcom.com (Dr. David N. Haney) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1861 HANEY ASSOCIATES wishes to announce the expansion of services to include program customization in computational chemistry: 1. Proprietary program customization: -new functions/algorithms -code cleanup/software engineering 2. Proprietary program interfaces: -interprocess communication (IPC) or other interfaces between proprietary codes or with commercial codes -graphical interfaces for proprietary codes 3. Proprietary program corporate support: -provide proprietary code in a corporate supportable package -support proprietary code to corporate user base -provide corporate training for proprietary code 4. Customize commercial codes: -literature or novel functions -interface with academic codes -source code modifications -Scripting: HTML, TCL, AWK, PERL, BCL, SPL, CHARMM -develop novel graphics viewers/builders/animators -develop simulation strategies, analysis applications -forcefield customization and parameter development 5. Perform custom simulations on proprietary problems. 6. Help establish client-server modeling for company user base. 7. UNIX tools for CPU load balancing in CPU-intensive groups. Please contact Dr. David Haney or visit http://www.i2020.net/edusoft/haney/haney.html. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From rull@rhino.chem.ruu.nl Tue Nov 7 04:46:54 1995 Received: from chemail.chem.ruu.nl for rull@rhino.chem.ruu.nl by www.ccl.net (8.6.10/950822.1) id EAA09645; Tue, 7 Nov 1995 04:44:09 -0500 Received: from rhino (rhino.chem.ruu.nl) by chemail.chem.ruu.nl with SMTP id AA00712 (5.67b/IDA-1.5 for <@chemail.chem.ruu.nl:chemistry@www.ccl.net>); Tue, 7 Nov 1995 10:45:19 +0100 Received: by rhino (931110.SGI/930416.SGI.AUTO) for @chemail.chem.ruu.nl:chemistry@www.ccl.net id AA29066; Tue, 7 Nov 95 10:43:24 GMT From: "Ton Rullmann" Message-Id: <9511071043.ZM29064@rhino.chem.ruu.nl> Date: Tue, 7 Nov 1995 10:43:19 +0000 Reply-To: rull@ruuci9.chem.ruu.nl X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: MachTen (Unix for Mac) Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi, Does anyone have experience with MachTen, a Unix port for Macintosh, and with the accompanying X Window Software ? (see http://www.tenon.com) Are you satisfied with the product? Any comments on ease-of-installation, compatibility, connectivity, performance? I will summarize the responses. Thanks! Ton Rullmann. -- J.A.C. Rullmann http://www-nmr.chem.ruu.nl/users/rull/rull.html Bijvoet Center for Biomolecular Research E-mail : rull@nmr.chem.ruu.nl Utrecht University, Padualaan 8, Phone : int+31.30.2533641 3584 CH Utrecht, the Netherlands Fax : int+31.30.2537623 ^ NOTE: phone numbers have changed - insert a 2 From netsci@awod.com Tue Nov 7 10:04:10 1995 Received: from sumter.awod.com for netsci@awod.com by www.ccl.net (8.6.10/950822.1) id JAA12625; Tue, 7 Nov 1995 09:50:48 -0500 Received: from [198.81.225.118] (ppp109.awod.com [198.81.225.118]) by sumter.awod.com (8.6.11/8.6.9) with SMTP id JAA11470; Tue, 7 Nov 1995 09:48:51 -0500 X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Nov 1995 11:06:56 +0000 To: chemistry@www.ccl.net From: netsci@awod.com (Network Science) Subject: November Issue of Network Science Cc: netsci@awod.com The November issue of NetSci is on-line at: http://www.awod.com/netsci This issue, which highlights mass screening, includes articles by John Brussolo and Sheila DeWitt (Parke-Davis Research), Barr Bauer (MDL Information Systems), Hugo Villar (Terrapin Technologies), Maryjo Zaborowski (Chiron Corp.) and Sheila DeWitt (Parke-Davis Research), Michael Lutz and J. Alan Menius (Glaxo-Wellcome Research Institute) and Roger Upton and Keith Davies (Chemical Design Ltd). From rosas@irisdav.chem.vt.edu Tue Nov 7 10:16:59 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/950822.1) id JAA12516; Tue, 7 Nov 1995 09:46:58 -0500 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id JAA04956; Tue, 7 Nov 1995 09:41:52 -0500 From: "Victor M. Rosas Garcia" Message-Id: <9511070941.ZM4954@irisdav.chem.vt.edu> Date: Tue, 7 Nov 1995 09:41:44 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Global minimum (philosophical) problems... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everybody, I'm just getting into the free energy calculation business, so I've been reading the most basic references (by van Gunsteren, Jorgensen, Mitchell and people like them). The first thing I noticed is that it is extremely important to make sure that one has a global minimum, together with all the conformers within certain energy; and it is very obvious that it is not easy to make sure that a conformer is "the" global minimum. I wonder if it is theoretically IMPOSSIBLE to prove that a given conformation is the global minimum. In my mind, is the same problem found when we want to say that we have found *all* the conformers within a certain energy range. Both (I think) boil down to proving a negative proposition (something that we *logically* cannot do), e.g. For the global minimum: "There are no other conformers with a lower energy than this one." For a distribution: "There are no other conformers that should be included in the population." Of course, it is always possible to *disprove* or *falsify* a negative proposition by showing a counterexample, but being unable to find a counterexample doesn't prove the truth of a negative proposition. OTOH, both of the propositions above can be cast in an affirmative form if we restrict them to a particular case, e.g.: For the global minimum, we could easily prove or disprove: "This particular conformer is higher in energy than the one we call 'global minimum'." By the same token, for a distribution: "This particular conformer has an energy higher than our cutoff limit of interest, (so we don't have to include it in the distribution)." So, I guess the point I'm trying to make is that we will *never ever* be sure of having "the" global minimum or a complete population because it is logically impossible to prove it. By running several conformational searches with different starting conditions we are probably doing the best we can. I'd like to know your opinions on this matter. PS Sorry if this stuff is too obvious, it isn't to me. Victor -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ------------------------------------------------------------------------- From guo@hyper.com Tue Nov 7 10:31:57 1995 Received: from www.hyper.com for guo@hyper.com by www.ccl.net (8.6.10/950822.1) id KAA13398; Tue, 7 Nov 1995 10:23:03 -0500 Received: (from guo@localhost) by www.hyper.com (8.6.9/8.6.9) id JAA00507; Tue, 7 Nov 1995 09:34:18 -0500 Date: Tue, 7 Nov 1995 09:34:18 -0500 From: Yufie Guo Message-Id: <199511071434.JAA00507@www.hyper.com> To: chemistry@www.ccl.net Subject: Chemistry conferences in China Cc: hyperchem@www.hyper.com Hi there, I am interested in finding out if there are any chemistry conferences held in China in the coming year. I can be reached by email. My email adress is guo@hyper.com Thank you in advance! Yufei Guo From xiaopeng@astro.ocis.temple.edu Tue Nov 7 10:46:58 1995 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id KAA13568; Tue, 7 Nov 1995 10:33:02 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id KAA29644; Tue, 7 Nov 1995 10:32:36 -0500 (EST) Date: Tue, 7 Nov 1995 10:32:34 -0500 (EST) From: Peking To: chemistry@www.ccl.net Subject: relaxed potential surface scan. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, CCls, Here is one of my problem: If you can kindly point out what did I do wrong and how can do this sucessfully, it will be very appreciated! I try to scan the potential surface of trans-2-chloro-butene. chose the coordinate of distance between Cl and H and the diherdral angle of Cl-C-C-H. But I got error termination with input z-matrix variables are not compatible with final structure.And I don't understand why the error message gives some info like "need constant BE=180.000". It seems that I didn't constrain a constaint. Below is my input file and the error message: #T uhf/sto-3g opt=addredundant nosymm test map the potential surface of tans-2-chloro-butene 0 1 C C, 1, R2 H, 1, R3, 2, A3 H, 1, R4, 2, A4, 3, D4, 0 H, 1, R4, 2, A4, 3, -D4, 0 C, 2, R6, 1, A6, 3 0., 0 H, 2, R7, 1, A7, 3, 180.,0 Cl,6, R8, 2, A8, 1, 0., 0 C, 6, R9, 2, A9, 1, 180.,0 H, 9, R10,6, A10,2, 0.0, 0 H, 9, R11,6, A11,2, D11, 0 H, 9, R11,6, A11,2, -D11,0 variables: R2=1.P5177985 R3=1.08427943 R4=1.08788173 R6=1.31402837 R7=1.08520688 R8=1.79377781 R9=1.52238446 R10=1.08556807 R11=1.08766724 A3=111.11087152 A4=110.07769389 A6=127.59575371 A7=115.61796491 A8=121.11489192 A9=125.91780168 A10=109.7704983 A11=110.53583184 D4=-120.64680338 D11=120.13192113 8 7 2.7058 S 10 -0.1 8 6 2 7 150.0 S 4 -10.0 However, I got the results Atom 5 needs variable 3= 1.0856605169 but is 1.0872659257 Atom 12 needs variable 9= 1.0870839612 but is 1.0848769525 Atom 5 needs variable 11=111.1688512850 but is 114.9193454953 Atom 12 needs variable 17=111.4980781622 but is 109.2370053341 Atom 5 needs variable-18=116.0001323360 but is 118.08122442940 Atom 6 needs constant BE= .0000000000 but is 93.8478831399 Atom 7 needs constant BE=180.0000000000 but is 77.9290399194 Atom 8 needs constant BE= .0000000000 but is -16.12445188058 Atom 9 needs constant BE=180.0000000000 but is 107.4156769479 Atom 10 needs constant BE= .0000000000 but is 61.5476759002 Atom 12 needs constant BE=-59.0905944184 but is 178.8397391217 input z-matrix are not compatible with final structure. xiaopeng ======================================================= Chemistry Graduate student 215-2047149(office) xiaopeng@astro.ocis.temple.edu ====================================================== From owner-chemistry@ccl.net Tue Nov 7 11:16:59 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA14271; Tue, 7 Nov 1995 11:16:46 -0500 Received: from rs2.hrz.th-darmstadt.de for schulte@ws09.pc.chemie.th-darmstadt.de by bedrock.ccl.net (8.7.1/950822.1) id LAA25110; Tue, 7 Nov 1995 11:16:31 -0500 (EST) Received: from ws09.pc.chemie.th-darmstadt.de by rs2.hrz.th-darmstadt.de with SMTP id AA44627 (5.65c/IDA-1.4.4 for ); Tue, 7 Nov 1995 17:16:02 +0100 Received: by ws09.pc.chemie.th-darmstadt.de (AIX 3.2/UCB 5.64/4.03) id AA21515; Tue, 7 Nov 1995 17:16:25 +0100 From: schulte@ws09.pc.chemie.th-darmstadt.de (Joachim Schulte) Message-Id: <9511071616.AA21515@ws09.pc.chemie.th-darmstadt.de> Subject: charge transfer in endohedral fullerenes To: chemistry@ccl.net Date: Tue, 7 Nov 1995 17:16:18 +0100 (CET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Ladies and Gentlemen, I am trying to calculate the electric field gradient of Sc in Sc@C82 with Gaussian 92. Until now I have used two relatively simple basis sets: 1) STO-3G (all electron calculation) 2) 3-21G for carbon and the Hay-Wadt ECP basis sets and ECP-potential for Sc. The ECP replaces 10 electrons. The basis set has been taken from P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). Both calculations have one common feature; they predict a quite low charge transfer from Sc to C82 (about 0.8 in the case of STO-3G and 1.6 with the second basis set). As a result an EFG is obtained which exeeds the measured one by a factor of about 20 in the STO-3G case and by a factor of roughly 10 with the Hay-Wadt basis set. The C82 cage geometry is C2 and the Sc-position is off-center by about 2 Angstroms. Also for other Sc positions the predicted charge transfer seems to be too low. Are there special basis sets which are suitable for ionic systems? Any helpful information on this topic would be highly appreciated. Sincerely Yours, Joachim Schulte From ui22204@sunmail.lrz-muenchen.de Tue Nov 7 12:32:00 1995 Received: from cd1.lrz-muenchen.de for ui22204@sunmail.lrz-muenchen.de by www.ccl.net (8.6.10/950822.1) id MAA16130; Tue, 7 Nov 1995 12:28:08 -0500 Received: from sun2.lrz-muenchen.de by cd1.lrz-muenchen.de; Tue, 7 Nov 95 16:55:38 +0100 Received: by sun2.lrz-muenchen.de (4.1/SMI-4.1) id AA24296; Tue, 7 Nov 95 16:55:37 +0100 Date: Tue, 7 Nov 1995 16:55:36 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 To: chemistry Subject: Re : CCL:PDBLib, a C++ macromolecular class library Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Several persons were unable to retrieve the document >from the URL I posted. I'm sorry: I should have given the full path: http://cuhhca.hhmi.columbia.edu/bourne.html This should work, as I was able the access the document just now. The name of the other library is pdb++. I have no data (and couldn't find any references via websearch(es)) to it, alas. Maybe other CCL participants have some information on pdb++ or similiar PDB OO libraries? -- Eugene From owner-chemistry@ccl.net Tue Nov 7 13:17:03 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA16531; Tue, 7 Nov 1995 13:04:26 -0500 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by bedrock.ccl.net (8.7.1/950822.1) id NAA26382; Tue, 7 Nov 1995 13:04:15 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA14720; Tue, 7 Nov 95 10:04:48 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma014717; Tue Nov 7 10:04:35 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA10514; Tue, 7 Nov 95 10:03:56 -0800 From: "Wayne Huang" Message-Id: <9511071003.ZM10512@mazda.wavefun.com> Date: Tue, 7 Nov 1995 10:03:55 -0800 In-Reply-To: Thomas Gray "Re: CCL:semiempirical calculations on a complex of Co and Sn." (Nov 7, 12:04am) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Thomas Gray Subject: Re: CCL:semiempirical PM3 Boron Parameters Cc: sparlist@wavefun.com, chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 7, 12:04am, Thomas Gray wrote: > Subject: Re: CCL:semiempirical calculations on a complex of Co and Sn. > Dear sir, > > I have been after boron parameters for PM3 for some time now. Would you > please send information or references (or both!) to my address? I would > be very interested in running some test calculations of these parameters > on carboranes and metallacarboranes. > Dear Thomas, Regarding your request for information on PM3 boron parameters, Here are some initial results. o Average Error for Geometries: PM3 AM1 ------------------------------------------- Bond Length 0.037 (146) 0.036 (141) Bond Angle 3.4 (30) 3.7 (30) o Average Error for Heat of Formation, Ionization Potential & Dipole Moment: PM3 AM1 MNDO -------------------------------------------------------- HF(71) 10.58 9.43 13.78 IP(26) 0.41 0.46 0.98 DM(23) 0.42 0.32 0.62 o A series boron compounds where AM1 fails geometrically have been corrected in this PM3 model. Both PM3 module (with new parameters for B and soon for Ca) and PM3(tm) (d-trnasition metals) have built in Spartan software. For further technical information, please contact support@wavefun.com New parameters can be found at: ftp://ftp.wavefun.com/pub/PARAMS While the manuscript is in preparation, reference can be cited as: Yu, J.; Hehre, W. J. To be published, Wavefunction, Inc., Irvine, California (1995). --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From GKELLOGG@Gems.VCU.EDU Tue Nov 7 14:02:03 1995 Received: from Gems.VCU.EDU for GKELLOGG@Gems.VCU.EDU by www.ccl.net (8.6.10/950822.1) id NAA17557; Tue, 7 Nov 1995 13:53:19 -0500 From: Received: from Gems.VCU.EDU by Gems.VCU.EDU (PMDF V5.0-3 #13707) id <01HXD46CBILC9LV4CQ@Gems.VCU.EDU> for CHEMISTRY@www.ccl.net; Tue, 07 Nov 1995 13:53:00 -0400 (EDT) Date: Tue, 07 Nov 1995 13:53:00 -0400 (EDT) Subject: HINT Software for Hydropathy/Hydrophobicty Modeling To: CHEMISTRY@www.ccl.net Message-id: <01HXD46CD4GI9LV4CQ@Gems.VCU.EDU> X-VMS-To: NET%"CHEMISTRY@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT eduSoft, LC wishes to announce the availability of new versions of HINT, the hydrophobicity software for modeling. HINT for Sybyl 6.2 is now available HINT for InsightII 95.0 will be available shortly HINT for Chem-X (July 95) is now available HINT calculates 3D hydropathy fields and 3D hydropathic interaction maps that are useful as tools for 3D QSAR and biomacromolecular structure, as well as: 1.estimates LogP for modeled molecules in InsightII, Sybyl, or Chem-X. 2.provides SMILES-based tools for molecule building using the Daylight Toolkit and the Biosym Sketcher module (available in Hint 2.1I). 3.numerically and graphically evaluates binding of drugs or inhibitors into protein structures and scores DOCK (UCSF) orientations. 4.constructs hydropathic (LOCK and KEY) complementarity maps that can be used to predict an ideal substrate from a known receptor or protein structure or to propose the hydropathic structure from known agonists or antagonists. 5.evaluates/predicts effects of site-directed mutagenesis on protein structure and stability. For more information please contact me, Dr. David Haney at haney@netcom.com, or view the HINT home page: http://www.i2020.net/edusoft/hint/hint.html Other WWW on-line info is available at: manuals http://www.phc.vcu.edu/hint/hintmans.html presentations: http://www.phc.vcu.edu/hint/hinttalk.html references: http://www.i2020.net/edusoft/hint/hintpubs.html ****************************************************************************** Dr. Glen E. Kellogg Department of Medicinal Chemistry eduSoft, LC Virginia Commonwealth University PO Box 1811 Richmond, VA 23298-0540 Ashland, VA 23005 Email: gkellogg@gems.vcu.edu ****************************************************************************** From A.T.Yagnik@exeter.ac.uk Tue Nov 7 14:47:02 1995 Received: from hermes for A.T.Yagnik@exeter.ac.uk by www.ccl.net (8.6.10/950822.1) id OAA18366; Tue, 7 Nov 1995 14:31:02 -0500 From: Received: from cen by hermes via ESMTP (TAA18092); Tue, 7 Nov 1995 19:28:27 GMT Message-Id: <866.199511071928@cen> Subject: SUMMARY: Book/review articles on forcefields. To: CHEMISTRY@www.ccl.net Date: Tue, 7 Nov 1995 19:28:25 +0000 (GMT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 6886 Hi everyone, Sometime ago, I posed this question to the CCL: >Hi, > >Does anyone out there know of a good book or review article on forcefields? >In particular, my colleagues are interested in any articles which may aid >in choosing the 'best' forcefield for a particular problem - if such a >thing exists (I know it is rather subjective, but they would appreciate any >leads). > >Thank you for your time. Well here's the summary many of you asked for. Sorry its taken a while - I was away/busy/etc. *Thank you very much* to all those who responded (I'm sorry I didn't thank you all at the time). Regards, Tosh. ====================================================================== Dear Tosh, We have recently finalized a study where we compared accuracies in energetic calculations for several current force fields. It will appear in J.Comput.Chem. in december. I think some of it also got inte one of the recent volumes (6 or 7) of Rev. Comp. Chem. In short, the conclusions are: don't trust force fields that use "general" parameters. The best results were obtained with reasonably true implementations of MM2 and MM3 (there are many around that call themselves MM2 or some such, you shouldn't always believe it), and also MMFF94. When it did not guess parameters, CFF91 gave good results. Among simple, harmonic, diagonal force fields, Amber* was outstanding (we didn't test true Amber). Sincerely, 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, peo@compchem.dfh.dk ________________________________________ You can look into "Reviews in Computational Chemistry": (1991), pp.81-97; 99-164;1-55; (1992) pp. 73-142. Good luck. ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## ________________________________________ I have been co-editing a book series called Reviews in Computational Chemistry. Several volumes have tutorial type descriptions about force fields. The latest one is focused on force fields for inorganics and organometallics by Clark Landis in Volume 6. It has references to other chapters on the topic you seek. The book is published by VCH Publishers Inc. Your library may have it. Kenny Lipkowitz ________________________________________ best is: @incollection{Lipkowitz:94, author = "", title = "", booktitle = "Reviews in Computational Chemistry", publisher = "VCH", volume = "I - IV", editor = "K. B. Lipkowitz and D. B. Boyd", pages = "", year = "1994", OPTnote = "eb--, lipkowitz@chem.inpui.edu", OPTannote = "SCI-book" } though it is actually 6 books. available in many libraries round the globe eb (Erich Bornberg-Bauer) _______________________________________ Tosh, We are in the process of evaluating and comparing several forcefields for use on carbohydrates. This work is currently being presented in the First Electronic Glycoscience Conference and will be published in the proceedings. If the molecules are anything like carbohydrates, let me know and I can send you all sorts of data. Abby Parrill Chemistry Department Artificial Intelligence in Chemistry Laboratory The University of Arizona abby@mercury.aichem.arizona.edu ______________________________________ I have collected literature recommendations from the net in http://www.amber.ucsf.edu/amber/ - follow 'info from the net'-> 'net texts' to see the index. Bill Ross ______________________________________ Tosh, have a look at Burkert & Allinger "Molecular Mechanics", ACS Monograph 177, 1982. More recent information can be found in Lipkowitz & Boyd "Reviews in Computational Chemistry", VCH, Vol. 2 (1991) and Vol. 6 (1995). Herbert Herbert Koeppen, PhD, Medicinal Chemistry Department, Boehringer Ingelheim KG, D-55216 Ingelheim, Germany phone: ++49-6132-776845, fax: ++49-6132-773418 e-mail: 100317.2656@compuserve.com _______________________________________ >Hi, > >Does anyone out there know of a good book or review article on forcefields? This is a BIG topic. Maybe some introductory text would help you. The best one I can recommend are the books (both small) by Fletcher and Powell. called "principles of Resrained minimization" and "principles of unrestrained minimization" respectively. Its a bit tough at first if you are not mathematically inclined. But it will give you a grounding in the principles that will serve you well IMHO. >In particular, my colleagues are interested in any articles which may aid >in choosing the 'best' forcefield for a particular problem - if such a >thing exists (I know it is rather subjective, but they would appreciate any >leads). I would look for all of the force field validation experiments that have been done. There are really not that many and I could give you some lead references if you like. The KEY here is to find validations that are CLOSE to what you want to use the force field for. Even proteins (I'm just making an assumption here based on your address.) differ from one another and the various force fields may also vary in their ability to reproduce/ "predict" the microstructure of the proteins. > >Thank you for your time. > >Regards, All views expressed here are only my own. Adi M Treasurywala Allelix Biopharma., 6850 Goreway Drive, Mississauga, Ontario. CANADA L4V 1V7. (905)677-0831 FAX (905)677-5344 ________________________________________ -- =============================================================================== Asutosh T Yagnik, Tel: (+44) 1392 263451 Protein Structure Group, Fax: (+44) 1392 263434 Department of Chemistry, Email: ATYagnik@exeter.ac.uk University of Exeter, * * WWW: http://www.exeter.ac.uk/ Stocker Road, Exeter. EX4 4QD. UK. > ~ATYagnik/ATYagnik \__/ {All opinions are my own!} "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi =============================================================================== From hinsenk@ERE.UMontreal.CA Tue Nov 7 15:47:03 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/950822.1) id PAA19543; Tue, 7 Nov 1995 15:46:05 -0500 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by condor.CC.UMontreal.CA with ESMTP id PAA04904 (8.6.11/IDA-1.6); Tue, 7 Nov 1995 15:43:43 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id PAA02595; Tue, 7 Nov 1995 15:43:41 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id PAA28143; Tue, 7 Nov 1995 15:43:40 -0500 Date: Tue, 7 Nov 1995 15:43:40 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199511072043.PAA28143@cyclone.ERE.UMontreal.CA> To: ui22204@sunmail.lrz-muenchen.de CC: chemistry@www.ccl.net In-reply-to: (message from Eugene Leitl on Tue, 7 Nov 1995 16:55:36 +0100 (MET)) Subject: Re: CCL:Re : PDBLib, a C++ macromolecular class library The name of the other library is pdb++. I have no data (and couldn't find any references via websearch(es)) to it, alas. Maybe other CCL participants have some information on pdb++ or similiar PDB OO libraries? PDB++ is available by ftp from cgl.ucsf.edu as /pub/libpdb++.shar; there is also a C version with the name /pub/libpdb.shar. All it does is handle line-by-line I/O of PDB files, so it saves you the trouble of having to deal with Fortran-formatted files from C or C++. If that's what you need, get a copy - it works. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From gregory@wucmd.wustl.edu Tue Nov 7 16:47:05 1995 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.10/950822.1) id QAA20647; Tue, 7 Nov 1995 16:36:53 -0500 Received: from wucmd by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id PAA28318; Tue, 7 Nov 1995 15:36:49 -0600 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@www.ccl.net id AA02353; Tue, 7 Nov 95 15:22:42 -0600 Date: Tue, 7 Nov 1995 15:08:03 -0600 (CST) From: Gregory Nikiforovich Subject: Re: CCL:Global minimum (philosophical) problems... To: "Victor M. Rosas Garcia" Cc: chemistry@www.ccl.net In-Reply-To: <9511070941.ZM4954@irisdav.chem.vt.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 7 Nov 1995, Victor M. Rosas Garcia wrote: > For the global minimum, we could easily prove or disprove: > "This particular conformer is higher in energy than the one we call 'global > minimum'." > By the same token, for a distribution: > "This particular conformer has an energy higher than our cutoff limit of > interest, (so we don't have to include it in the distribution)." > Since I like philosophical problems, let me comment. As far as we are interested in conformers (like in conformational search problem), energy is just a target function, and energy minimization is a way to find a conformer, i.e., a particular 3D arrangement of atoms/functional groups. If you look at the problem from this side, you would notice that several very similar 3D arrangements may possess different energies. On the other hand, some very different 3D arrangements can possess almost identical energies (e.g., enantiomers). So the true task of conformational search is not to find all conformers within a given cutoff; it is to find all different 3D arrangements within a given energy cutoff. This task is much more realistic, since the possibility of missing a really different 3D arrangement during any search is less than to miss a minimum close to "the global" one in energy. However, it is not philosophy any more... Best wishes. Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130