From toukie@zui.unizh.ch Mon Nov 4 04:18:46 1996 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.2/950822.1) id EAA19133; Mon, 4 Nov 1996 04:10:03 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA10439; Mon, 4 Nov 1996 10:14:18 +0100 Message-Id: <1.5.4.32.19961104091045.0066d4dc@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 04 Nov 1996 10:10:45 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Polarisability in MOPAC Dear Colleagues; Using MNDO with MOPAC 6.0, I obtained an E4 average alpha polaris- ability value for phenol of 11.261823 cubic Angstoms. According to the in- formation available to me, the E4 value is derived from the effect of the applied electric field (electric field gradient of 0.001) on the heat of formation. Is the "electric field gradient of 0.001" abbreviated "del E = 0.001"? Also, what are the units/dimensions of the value "0.001"? Thanks in advance to all responders. Sincerely, S. Shapiro ZH, CH toukie@zui.unizh.ch From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Mon Nov 4 07:18:40 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.2/950822.1) id GAA19882; Mon, 4 Nov 1996 06:40:57 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA03044 for ; Mon, 4 Nov 1996 12:36:05 +0100 (MET) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id NAA25004 for chemistry@www.ccl.net; Mon, 4 Nov 1996 13:38:35 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611041338.ZM25000@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 4 Nov 1996 13:38:34 +0100 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: Summary: Quntom Chem. MD Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de" --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u Dear Netter Enclosed I collect the responses to my question about quantom chemical molecular dynamics. Thanx all for their answers. The question: ************* I want to know if there is any program applying semiempirical and/or ab i= nitio quantom chemical calculation in molecular dynamics simulation. Any relate= d information and comments is highly appreciated. *************************************************************************= *** Recent academic versions of CHARMM have both AM1 (semi-empirical) and GAMESS (ab-initio) interfaces and code; distribution is arranged through Prof. Martin Karplus's group at Harvard for a modest fee to non-profit research organizations. -- Rick Venable =3D=3D=3D=3D=3D\ |=3D| "Eschew Obfus= cation" FDA/CBER Biophysics Lab |____/ |=3D| Bethesda, MD U.S.A. | \ / |=3D| ( Not an official stateme= nt or rvenable@deimos.cber.nih.gov \/ |=3D| position of the FDA; fo= r that, http://nmr1.cber.nih.gov/venable.html |=3D| see http://www.fda.go= v ) *************************************************************************= ** Hi! Charmm will do just that. Charmm 24b2 should do the ab-initio stuff - bu= t I found a bunch of routines missing when I tried to compile. The am1 method is quite stable now. There are numberous others - but that one is availible commercially (for the am1 at least) and straight forward. Good luck 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 | ------------------------------------------------------------------- *************************************************************************= ** You might have a look at: Bash P. A., Ho L. L., MacKerell A., Levine D., Halstrom P., =93Progress Toward Chemical Accuracy in Computer Simulations of Condense= d Phase Chemical Reactions=94, Proc. Nat. Acad. Sci., 93, 3698, 1996 Ho L. L., MacKerell, A., Bash P. A. =93Proton and Hydride Transfers in Solution: Hybrid QM/MM Free Energy Perturbation Study=94, J. Phys. Chem., 100, 4466, 1996 Paul Bash ________________________________________ Paul A. Bash Argonne National Laboratory Bldg 202/A349 9700 S. Cass Avenue Argonne, IL. 60439 pabash@anl.gov Work Phone: 708-252-8631 Home Phone: 312-642-3029 Fax: 708-252-3387 ---------------------------------------- *************************************************************************= ** There are probably more, but the two I am aware of off hand are Carr-Parinello, which does dynamics with the local density functional approximate ab initio code, and some work by Dave Dixon, while at Dupont,= which he as reported at ACS meetings. It's been some time, but the Corne= ll Theory Center had the Carr-Parinello code, and Dave Dixon is now at Pacif= ic Northwest Laboratories I believe. I would be interested in hearing a summary, if there isn't already one in= the CCL archives. Thanks. EC --- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb *************************************************************************= ** HyperChem 4 (semiempirical level), 4.5-5 both ab initio and semiempirical= - but of cours it's comercial. If it's still interesting I can ad some comm= ents. regards, Krzys Radacki _________________________-----------------------------------------------= ----- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE= --- ------------------------------------------------------------------------= ----- *************************************************************************= ** Try HyperChem (available for both IBM-compatible PC and for SGI). The URL is http://www.hyper.com Dan Berger bergerd@bluffton.edu *************************************************************************= ** Hi Emad, I am not entirely sure what you mean with your request... However, I know that "combined QM/MM" (a method where the most interestin= g part of the molecule is being treated by QM, e.g. DFT, the rest by MM) is very actively under study these days. No references, though. On the other hand, there is the "ab initio molecular dynamics", as has been developed by Car and Parinello. References that I would have on hand would be P.E. Blochl, Phys.Rev.B.50 (1994), 17953 and other papers by Blochl (the name contains an "Umlaut o"). D.K.Remler, P.A.Madden, Mol. Phys. 70 (1990), 921 (review paper). Look, of course, also for papers by M.Parinello and / or R.Car. Hope this helps a bit.... Please summarize! Yours, Georg This is a P.S. to my message that I sent before: one should call the Car-Parinello approach "first principle molecular dynamics" since it is a DFT based method rather then an "ab initio" method. G. -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalga= ry.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D *************************************************************************= ** HyperChem can do this; I can send you more information, or put you in contact with a local dealer, if you wish. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-404= 0 Info requests to: info@hyper.com Support questions to: support@hyper.c= om Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ *************************************************************************= ** Contact or search for papers by Paul Bash at Argonne National Laboratory,= Argonne, IL, USA. He has been doing work in that area for years. -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** *************************************************************************= ** Dear Emad, I read your note on Computational Chemistry List (CCL). I am presently applying ab initio molecular dynamics on biological systems. The method, who allow you to solve the time-dependent Sro equation in simulations a smart way, was devised 11 years ago by Car and Parrinello, If you're interested, I can send you some reprints. Sincerely yours Paolo -- Paolo Carloni IBM Zurich Research Laboratory Saeumerstrasse 4 CH-8803 Rueschlikon/Switzerland Internet: cap@zurich.ibm.com Phone: +41-1-724-8490 Fax: +41 1-724 0809 *************************************************************************= ** Thanx again. -- = Emad ********************************************************************* E. Tajkhorshid = German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de-- From ccl@www.ccl.net Mon Nov 4 12:18:46 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id MAA22811; Mon, 4 Nov 1996 12:18:17 -0500 (EST) Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by bedrock.ccl.net (8.8.2/950822.1) id MAA01559; Mon, 4 Nov 1996 12:18:12 -0500 (EST) From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA23147 (5.67b/IDA-1.5 for <@kodakr.kodak.com:chemistry@ccl.net>); Mon, 4 Nov 1996 12:17:18 -0500 Received: from xd88.kodak.com by euler.kodak.com via SMTP (940816.SGI.8.6.9/940406.SGI) id MAA27041; Mon, 4 Nov 1996 12:17:42 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA16309; Mon, 4 Nov 1996 12:17:42 -0500 Date: Mon, 4 Nov 1996 12:17:42 -0500 Message-Id: <9611041217.ZM13235@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: Statistics Cc: mckelvey@kodakr.kodak.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: Quite often we need to do some statistical model building after doing MO calculations. In the midst of this there is the need to look for the best model under the "all-possible-subsets" (APS) scheme. The rub is that I do not know of any commercial packages that will permit doing such a search. The search is basically to look for all possible models for M experimental data points, and with the free predictors to be searched over to be greater than M. Obviously one can only correctly determine M-1 models, assuming the usual free fitting constant. Currently I often have have ~2M free predictors. Yes, I have tried PLS, but I find it to be stochiastic. The best model will change sometimes for the worse if more free predictors are added, for example, whereas traditional APS will not. I have looked at the packages SAS and Minitab. Neither of these packages will do this. I have one batch oriented package that runs on an SGI power challenge that turns out to be slower than Minitab on my 90 Mhz Pentium! Any suggestions would be greatly appreciated. Thanks! John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From ccl@www.ccl.net Mon Nov 4 13:30:55 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id MAA23037; Mon, 4 Nov 1996 12:46:32 -0500 (EST) Received: from bioc1.msi.com for mjf@msi.com by bedrock.ccl.net (8.8.2/950822.1) id MAA02283; Mon, 4 Nov 1996 12:46:30 -0500 (EST) Received: from iris70.msi.com by bioc1.msi.com (5.64/0.0) id AA05285; Mon, 4 Nov 96 09:45:55 -0800 Received: by iris70.msi.com (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id JAA16172; Mon, 4 Nov 1996 09:45:11 -0800 Date: Mon, 4 Nov 1996 09:45:11 -0800 From: mjf@msi.com (Mark J Forster ) Message-Id: <199611041745.JAA16172@iris70.msi.com> To: chemistry@ccl.net Dear Emadeddin In response to your question on quantum chemical MD I should point out two MSI products that might be of interest. QuanteMM is a hybrid QM/MM code that treats the molecular mechanics portion of a system using Discover_3, while small regions of interest that need to be treated by quantum mechanics can use Turbomole, Dmol or MOPAC. The QuanteMM module is accessed through the insightII interface. Current capabilities allow for single point minimization and geometry optimzation. Fast_Struct/Sim_Ann is a high speed DFT based code that can be used for the calculation of energy, gradients, geometry optimization and for simulated annealing MD studies. Again Fast_Struct/Sim_Ann is accessible via the insightII interface. Best Wishes Mark J Forster Manager Protein Applications Product Development Molecular Simulations Inc. 9685 Scranton Rd, San Diego, CA 92121, USA. Phone (619) 458 9990 FAX (619) 458 0136 e-mail: mjf@msi.com WWW: http://www.msi.com/ From jerry@Ramsey.chem.dal.ca Mon Nov 4 17:18:48 1996 Received: from Ramsey.chem.dal.ca for jerry@Ramsey.chem.dal.ca by www.ccl.net (8.8.2/950822.1) id RAA25399; Mon, 4 Nov 1996 17:11:14 -0500 (EST) Received: by Ramsey.chem.dal.ca (940816.SGI.8.6.9/940406.SGI.AUTO) id SAA12878; Mon, 4 Nov 1996 18:16:23 -0400 Date: Mon, 4 Nov 1996 18:16:09 -0400 (AST) From: "Jerry C.C. Chan" To: CHEMISTRY@www.ccl.net Subject: Any NMR data processing freeware for Indy? In-Reply-To: <199610310914.AA14419@uscmail.usc.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Could anyone please recommend a versatile NMR data processing freeware for Indy (IRIX 5.3)? Many thanks, Jerry Chemistry Department Dalhousie University