From johannes.zuegg@anu.edu.au Fri Jul 31 03:03:58 1998 Received: from anugpo.anu.edu.au (anugpo.anu.edu.au [150.203.2.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA27931 Fri, 31 Jul 1998 03:03:56 -0400 (EDT) Received: from hannes.anu.edu.au (hannes.anu.edu.au [150.203.193.229]) by anugpo.anu.edu.au (8.8.8/8.8.8) with SMTP id RAA11408 for ; Fri, 31 Jul 1998 17:03:54 +1000 (EST) Message-Id: <199807310703.RAA11408@anugpo.anu.edu.au> From: "Johannes Zuegg" Organization: JCSMR To: CHEMISTRY@www.ccl.net Date: Fri, 31 Jul 1998 17:01:23 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Hydrophobic Solvent-box needed Reply-to: johannes.zuegg@anu.edu.au Priority: normal Dear CCL-Net, I would like to simulated my model in a hydrophobic solution, and I am on my way to generate a equilibrated hexan solvent-box in AMBER. But as the equilibrium of such a solvent box takes a long time, I wonder if the coordinates of equilibrated hydrophobic solvent-boxes (not only hexan) are somehow available, or who already did such calculations ? Thanks for any suggestions Johannes --------------------------------------------------------------------- John Curtin School of Medical Research Australian National University Dept. Biochemistry and Molecular Biology PO Box 334 Canberra, ACT 2612, Australia Tel: +61 2 6279 8301 Fax: +61 2 6249 0415 EMail: johannes.zuegg@anu.edu.au --------------------------------------------------------------------- From destack@unomaha.edu Fri Jul 31 09:05:19 1998 Received: from s-cwis.unomaha.edu (s-cwis.unomaha.edu [137.48.1.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA00920 Fri, 31 Jul 1998 09:05:17 -0400 (EDT) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id IAA15189 for ; Fri, 31 Jul 1998 08:00:52 -0500 (CDT) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 31 Jul 98 08:05:16 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 31 Jul 98 08:05:09 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 31 Jul 98 08:05:06 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BDBC5A.83BF6900@zinc.unomaha.edu>; Fri, 31 Jul 1998 08:09:17 -0500 Message-ID: <01BDBC5A.83BF6900@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" Subject: Summary: Atomic charges Date: Fri, 31 Jul 1998 08:09:16 -0500 Return-Receipt-To: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id JAA00920 Thanks to all who responded to this thread. A theme derived from the responses is that natural charges, because the converge with increasing basis set size, may be more appropriate in describing charges distribution when high level calculations are performed. The original question: > Dear Cclers, > > In doing some B3LYP/6-31G* calculations on a medium size carbocation radical (ca. 330 basis sets), I find significant differences in the natural atomic charges when compared to Mulliken or electrostatic charges. A straightforward discussion of atomic charges is presented in "Practical Strategies for Electronic Calculations" by Hehre. This discussion describes two general methods; partitioning schemes, e.g. Muillken charges, and fitting schemes, e.g. electrostatic charges. > > I have the following questions: > Are natural charges calculated by a partitioning scheme or a fitting scheme? > > Given that partitioning schemes don't converge with increasing basis set size, which method is best suited for B3LYP/6-31G* with 300+ basis sets? > > Are there any other good discussions (references) on how natural charges are generated? Do they converge with increasing basis set size? > > Which method is would one use in comparing charges of two carbon atoms, one with a hydrogen, one without? > > Another point of confusion about the charges obtained in this calculation, while the electrostatic charges show a low concentration at a certain carbon, a map of the electrostatic potential on to the total electron density shows a significant positive charge in the region around this same carbon. Since electrostatic charges are derived from a fitting scheme, shouldn't they mirror the map of the electrostatic potential on to the total electron density? > > I'll summarize this thread. Response #1: NAO charges are derived from diagonalizations of sub-blocks of the density matrix. They converge as the quality of the wave function (basis set and amount of EC) is improved. Fitted charges have the problem that the atoms near the surface of the molecule are the main contributers to the electrostatic potential, thus atomic charges within the molecule are not very well defined. NAO charges are attractive for analysis purposes, as presumably is your interest, but fitted charges should be used for force field modelling. Another possibility for analysis is the AIM approach, but this is computationally much more involved. Chem. Rev. vol 88, 899 is a good review of NAO. Frank Response #2: I don't think there is such a thing as a "natural charge" of an atom in a molecule. In reality you have a charge density everywhere around atoms and along bonds. Assigning atomic charges means approximating this density by a set of point charges. Partitioning schemes try to provide a approximation that conserves the relative electronic densities around the atoms. Fitting provides the charges that best approximate the interactions of the molecule with its surroundings. The fact that the two schemes can yield rather different answers means that a point charge model is in general not a good approximation to the real charge density. But I wouldn't call one or the other approach more natural. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais Response #3: Dear Prof. Stack, NBO (Natural) Charges are much better behaved than Mulliken Charges. They are based on a basis set transformation, thereby avoiding the partitioning problem. In fact, the partitioning is achieved by transforming the basis functions into a set of orthogonal basis functions under the side-condition of changing basis functions of low occupancy more than basis functions of high occupancy. Natural charges are only slightly dependent on basis sets and - as far as I remember - converge smoothly to the limit of complete basis sets. I prefer Natural Charges, since they fit to chemical intuition and have several advances over Mulliken charges. In addition, Natural Localized MOs (NLMOs) - at a later stage of the NBO analysis - are an excellent method to describe (hyper)conjugation. Literature: Reed, Weinstock, Weinhold, J. Chem. Phys. 1985, 83, 735. Maseras, Morokuma, Chem. Phys. Lett. 1992, 192, 500. Stefan Fau --------------------------------------------------- Stefan Fau fau@mailer.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg Hans-Meerwein-Str. D-35032 Marburg Response #4: >>Are natural charges calculated by a partitioning scheme or a fitting scheme? Natural charges come from a population analysis. They are distant relatives of the Mulliken type analysis. >>Given that partitioning schemes don't converge with increasing basis set size... Not true. The neat thing about natural charges is that they DO CONVERGE. >>which method is best suited for B3LYP/6-31G* with 300+ basis sets? That depends on you. Electrostatic charges are an obvious choice if you want to study intermolecular interactions (e.g. parameterize a force field) or reproduce dipole moments (Natural charges are not good at that I'm told). But they can give results that differ drastically from "normal" expectations. Natural charges are a better choice (IMHO) if you want to look at and compare electron distributions. Both methods will work just fine with the calc you propose (B3LYP/6-31G*). The best all around discussion of charge calculations and their pitfalls is given in a recent review article by Steve Bachrach. It was published in Reviews of Computational Chemistry, Lipkowitz and Boyd, eds., but I don't have the volume or page. Finally, the example you gave is just one of the many "problems"one encounters when using electrostatic charges. People naturally expect the charges to mirror electrostatic potential maps and they often don't. The reason is that the potential shown on the map is derived from the entire molecule and not just the closest atom. You can easily convince yourself that non-nearest neighbors can make significant contributions to the potential at a given point in space by doing a test calculation on a molecule with a "distant" polar group. Have fun. Alan ------------- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan Thanks again all! Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From jmolmod@as1200.organik.uni-erlangen.de Fri Jul 31 10:36:31 1998 Received: from faui45.informatik.uni-erlangen.de (root@faui45.informatik.uni-erlangen.de [131.188.2.45]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA01515 Fri, 31 Jul 1998 10:36:26 -0400 (EDT) Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by faui45.informatik.uni-erlangen.de (8.9.1/8.1.41-FAU) with ESMTP id QAA05304 for ; Fri, 31 Jul 1998 16:36:20 +0200 (MET DST) Received: (from jmolmod@localhost) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) id QAA16130 for chemistry@www.ccl.net; Fri, 31 Jul 1998 16:34:21 +0200 (MET DST) From: Journal of Molecular Modeling Message-Id: <199807311434.QAA16130@as1200.organik.uni-erlangen.de> Subject: J.Mol.Model.: BioMedLink Award To: chemistry@www.ccl.net Date: Fri, 31 Jul 1998 16:34:20 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text OFFICE MEMO Date: 31/07/1998 BioMedLink Award Dear colleague, The 'Journal of Molecular Modeling' Internet site at http://www.ccc.uni-erlangen.de/jmolmod has been included in the BioMedLink database. The editorial board of BioMedLink has rated the site particularly interesting. BioMedLink is an evaluated and annotated database of Internet resources for the bio/medical community jointly created by BioMedNet (http://biomednet.com) and the University of Indiana. New entries are added weekly, and existing entries are reviewed and rated by our editorial board. BioMedLink has been described as 'the Yahoo for biological and medical researchers'. You can view the entry of the 'Journal of Molecular Modeling' at: http://biomednet.com/db/biomedlink/BMLK.13130 We would like to invite you to have a look by yourself and to browse through the pages of the 'Journal of Molecular Modeling'. If you do have any question, the members of the editorial office will be pleased to help you. Sincerely Yours, Tim Clark Henryette Roth (editor-in-chief) (assistant editor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-6567 ^ ^ Computer-Chemie-Centrum ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ http://www.ccc.uni-erlangen.de/jmolmod ^ http://link.springer.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ JOURNAL OF MOLECULAR MODELING - YOU MAKE THIS JOURNAL A SUCCESS From castejon@kbw350.chem.yale.edu Fri Jul 31 10:57:01 1998 Received: from kbw350.chem.yale.edu (kbw350.chem.yale.edu [130.132.25.45]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA01712 Fri, 31 Jul 1998 10:57:00 -0400 (EDT) Received: by kbw350.chem.yale.edu (AIX 3.2/UCB 5.64/4.03) id AA13752; Fri, 31 Jul 1998 10:55:53 -0400 Date: Fri, 31 Jul 1998 10:55:53 -0400 From: castejon@kbw350.chem.yale.edu (Henry J. Castejon) Message-Id: <9807311455.AA13752@kbw350.chem.yale.edu> To: CHEMISTRY@www.ccl.net, calculations@www.ccl.net, of@www.ccl.net, structure@www.ccl.net, surfaces@www.ccl.net Subject: electronic Hello everyone: First of all, I would like to thank to all who answer my quetion about the transition metals. I really appreciate these inputs. Some of the answers raised a question. This is: how about if instead of having a huge catalyst and have a surface. Can JAGUAR (which was the most recommended software in all answers) do calculations of metalic surfaces? Thanks a lot again for your insights? Henry. From asnmaz01@asc.edu Fri Jul 31 12:30:53 1998 Received: from vera.dpo.uab.edu (Vera.dpo.uab.edu [138.26.1.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA03634 Fri, 31 Jul 1998 12:30:52 -0400 (EDT) Received: from asc.edu (138.26.15.137) by vera.dpo.uab.edu (LSMTP for Windows NT v1.1a) with SMTP id <0.AD4190C0@vera.dpo.uab.edu>; Fri, 31 Jul 1998 11:30:53 -0500 Sender: root@www.ccl.net Message-ID: <35C1F14C.52B2D6FC@asc.edu> Date: Fri, 31 Jul 1998 11:31:08 -0500 From: "Mark A. Zottola" Organization: Alabama Supercopmuter Center X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.0.34 i686) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: AMBER Help Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am attempting to study the dynamics of a novel hydrogen bonded system using AMBER. However, I am unable to ascertain from the documentation how I can have the program cumulatively store the coordinates. I would like the updated coordinates appended to a restart file instead of overwriting the restart file. Any suggestions on how to accomplis this would be very welcome! Thanks! -- ********* Mark A. Zottola Alabama Research and Education Network 119 Rust Research Center Nichols Research Corporation University of Alabama-Birmingham VOICE: (205) 934-3893 Birmingham, AL 35294 EMAIL: asnmaz01@csimail.asc.edu From efremov@nmr.ru Fri Jul 31 12:56:30 1998 Received: from ultra.nmr.ru (ultra.nmr.ru [194.85.8.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA03863 Fri, 31 Jul 1998 12:56:27 -0400 (EDT) Received: from nmr.ru (pcmult [194.85.8.53]) by ultra.nmr.ru (8.9.0/8.9.0) with ESMTP id UAA10420 for ; Fri, 31 Jul 1998 20:56:15 +0400 (MSD) Message-ID: <35C1F79D.B023E4B3@nmr.ru> Date: Fri, 31 Jul 1998 20:58:05 +0400 From: Efremov X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: NMA dimer Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCLers, I am interesting in getting coordinates or Z-matrix of NMA dimer optimized using high-level ab initio calculations. It seems that numerous such studies have been done in the past. I would appreciate your responses and comments. Regards. Roman Efremov From intsim.com!haun@news.cts.com Fri Jul 31 14:18:25 1998 Received: from mh2.cts.com (mh2.cts.com [209.68.192.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA04924 Fri, 31 Jul 1998 14:18:24 -0400 (EDT) Received: from king.cts.com (root@king.cts.com [198.68.168.21]) by mh2.cts.com (8.8.7/8.8.5) with ESMTP id LAA26863 for ; Fri, 31 Jul 1998 11:18:24 -0700 (PDT) Received: from donews.cts.com (donews.cts.com [192.188.72.21]) by king.cts.com (8.8.7/8.8.7) with SMTP id LAA17607 for ; Fri, 31 Jul 1998 11:18:23 -0700 (PDT) Received: from intsim.com by donews.cts.com with uucp (Smail3.1.29.1 #5) id m0z2Jl0-0000DXC; Fri, 31 Jul 98 11:18 PDT Received: from topi.intsim.com by zebra.intsim.com via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA27650; Fri, 31 Jul 98 11:06:34 -0700 Message-Id: <9807311806.AA27650@zebra.intsim.com> X-Sender: haun@zebra.intsim.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Fri, 31 Jul 1998 11:19:20 -0700 To: CHEMISTRY@www.ccl.net From: Dan Haun Subject: SCULPT version 2.6 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi All, Interactive simulations Inc. is pleased to announce the release of a much more robust version of SCULPT. Time-limited trial copies of version 2.6 and its manual are now available for review on our web site at http://www.intsim.com The new features are: * Active X / Ole embedding (for MS 97). * Ribbons. * Improvements on 2D-3D conversion of small stereo isomers. * Hot-linking with Chime beta 2.0 * Commands for rigid body translation and rotation. * Improvements on the graphical user interface which includes floating windows. SCULPT still continues to offer the interactive capabilities of overlaying one or more molecules, twisting and turning molecular structures, energetically docking ligands, exploring the packing of secondary structures, real-time minimization, visualizing of H-bond electrostatics and van der Waals forces. SCULPT allows the user to create annimations by recording quick time movies. Hardware requirements for SCULPT are Pentium-grade PCs with a minimum of 16MB of Memory and 10MB on the hard drive. SCULPT v.2.5 is also available for the PowerMac and version 2.1 is available forSGI platforms. Sincerely yours, Dan Haun Daniel P. Haun Tel: (619) 658-9462 Interactive Simulations Inc. Toll Free: (888) 272-8578 5330 Carroll Canyon Rd. Email: haun@intsim.com San Diego, CA 92121 Fax: (619) 658-9463 Web site http://www.intsim.com From shenkin@still3.chem.columbia.edu Fri Jul 31 14:31:52 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA05151 Fri, 31 Jul 1998 14:31:51 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id OAA12139; Fri, 31 Jul 1998 14:31:51 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id OAA13642; Fri, 31 Jul 1998 14:31:50 -0400 From: "Peter Shenkin" Message-Id: <9807311431.ZM13640@still3.chem.columbia.edu> Date: Fri, 31 Jul 1998 14:31:49 -0400 In-Reply-To: "Paddy Kane" "Monte Carlo: Request For Key Papers" (Jul 31, 11:30am) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "Paddy Kane" , "sp" , "mmod " , "CCL" Subject: Re: Monte Carlo: Request For Key Papers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Please see our on-line bibliography for the methods we support. -P. -- ************ "Yeah, but poverty can't buy happiness, either." ************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From bausch@chem.vill.edu Fri Jul 31 14:41:30 1998 Received: from rs6chem.chem.vill.edu (rs6chem.chem.vill.edu [153.104.73.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA05299 Fri, 31 Jul 1998 14:41:28 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with ESMTP id OAA08714 for ; Fri, 31 Jul 1998 14:41:24 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 31 Jul 1998 14:44:13 -0400 To: chemistry@www.ccl.net From: "Joseph W. Bausch" Subject: Seeking experiences with DQS Hi, I've recently put together a handful of linux boxes for our department to serve as compute machines primarily for running Gaussian. I have also got up and running the Distributed Queueing System out of Florida State University, with the hopes it can help with management of job submissions. I am hoping there are others in the CCL-world that have done this as well and can pass along their comments/experiences, in particular in the following area: -it was relatively straightforward to set up a complex so people can submit a G94 job to the complex, then the job gets sent to the least busy computer of our group of linux machines. However, what I don't know how to handle is dealing with checkpoint files and scratch files. If a person submits a job that goes to computer A and runs successfully, then wants to run another job using the same checkpoint file, how do you handle this with dqs? If the job gets submitted to say computer B, the checkpoint file isn't there, but instead is on computer A. I guess what I really want to have is the following: have all users just have to log into one machine, submit their Gaussian jobs from there, then somehow have their output and checkpoint files (when a job is complete) be copied back onto that one computer, with the ability to submit another job to the complex that might require the use of the checkpoint file. Right now I don't have the computers in the complex sharing any hard drives, except for the files needed to run DQS, and this is done via NFS. Any advice/comments would be appreciated. I'll summarize if there is sufficient interest. Joe bausch@chem.vill.edu -------------------- From seabra@NPD.UFPE.BR Fri Jul 31 09:34:17 1998 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA01146 Fri, 31 Jul 1998 09:34:07 -0400 (EDT) Received: from danon (Danon.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01J01PNPD5R4000SXE@NPD.UFPE.BR> for chemistry@www.ccl.net; Fri, 31 Jul 1998 10:30:39 GMT-3 Date: Fri, 31 Jul 1998 10:41:24 -0300 From: Gustavo de Miranda Seabra Subject: Summary: Computer simulaion methods To: Computational Chemistry List , p_kane@mailcity.com, s.m.todd@chem.hull.ac.uk Reply-to: Gustavo de Miranda Seabra Message-id: <009c01bdbc88$e9317a70$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_0099_01BDBC6F.C39956C0" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_0099_01BDBC6F.C39956C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Please forgive me for the late in posting this summary but, at = least, it's here. My questios was: Does anyone have references that compare various simulation = methods, like ab-initio, semi empirical, molecular dynamics and monte-carlo? And here are the replyes I've received: 1) From Pat Hogue (PHogue@space.honeywell.com) I suggest Tim Clark's book A Handbook of Computational Chemistry, A Practical Guide to Chemical Structure and Energy Calculations, John=20 Wiley and Sons (1985) ISBN 0-471-88211-9. It is a bit dated but = still=20 a very good reference. 2) Klaus Stark (kstark@msicam.co.uk) I'm sure Dr. Erich Wimmmer's paper "Computational Methods For Atomistic Simulations" at http://www.msi.com/info/materials/general/erich/Main.htm will be of great value for you. 3) Phillipe Chavatte (pchavatt@phare.univ-lille2.fr)=20 I give you three references concerning your request : Howard A.E., Kollman P.A. An analysis of current methodologies for conformational searching of complex molecules J. Med. Chem., 1988, 31,9, 1669-1675. Cohen N.C., Blaney J.M., Humblet C., Gund P., Barry D.C. Molecular modeling software and methods for medicinal chemistry J. Med. Chem., 1990, 33,3, 884-894. Lesyng B., McCammon J.A. Molecular modeling methods basic techniques and challenging problems Pharmac. Ther., 1993, 60, 149-167. 4) Dave Young (youngd2@mail.auburn.edu) I have some introductory descriptions on the web at=20 http://www.auburn.edu/~youngd2/topics/contents.html Thanks to everyone. -------------------------------------------------------------------------= ------------------ Gustavo de Miranda Seabra MSc Student in Chemistry seabra@npd.ufpe.br Federal University of Pernambuco Brazil -------------------------------------------------------------------------= ------------------ ------=_NextPart_000_0099_01BDBC6F.C39956C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 all,
 
    Please forgive me for the late = in posting=20 this summary but, at least, it's here.
 
My questios=20 was:
 
        Does = anyone have=20 references that compare various simulation methods,
    like ab-initio, semi empirical, molecular = dynamics and=20 monte-carlo?
 
And here are=20 the replyes I've received:
 
1) From Pat = Hogue (PHogue@space.honeywell.com= )
    I suggest Tim Clark's = book A=20 Handbook of Computational Chemistry, A
    Practical = Guide to=20 Chemical Structure and Energy Calculations, John
    = Wiley=20 and Sons (1985) ISBN 0-471-88211-9.  It is a bit dated but still=20
    a very good reference.
 
2) Klaus Stark = (kstark@msicam.co.uk)
    I'm sure Dr. Erich = Wimmmer's=20 paper
    "Computational Methods For Atomistic=20 Simulations" at
    http://= www.msi.com/info/materials/general/erich/Main.htm
  &nbs= p;=20 will be of great value for you.
 
3) Phillipe=20 Chavatte (pchavatt@phare.univ-lille2.= fr) =
    I give you three = references=20 concerning your request :

    Howard A.E., Kollman = P.A.
    An analysis of current methodologies for=20 conformational searching of
    complex=20 molecules
    J. Med. Chem., 1988, 31,9,=20 1669-1675.

    Cohen N.C., Blaney J.M., Humblet = C., Gund=20 P., Barry D.C.
    Molecular modeling software and = methods for=20 medicinal chemistry
    J. Med. Chem., 1990, 33,3,=20 884-894.

    Lesyng B., McCammon=20 J.A.
    Molecular modeling methods basic techniques = and=20 challenging problems
    Pharmac. Ther., 1993, 60,=20 149-167.
 
4) Dave Young=20 (youngd2@mail.auburn.edu)
    I have some introductory = descriptions on=20 the web at
    http://www.a= uburn.edu/~youngd2/topics/contents.html
 
 
Thanks to=20 everyone.
----------------------------------------------------------------= ---------------------------
       =             &= nbsp; =20 Gustavo de Miranda Seabra
MSc Student in=20 Chemistry          &nbs= p;      =20 seabra@npd.ufpe.br
Federal = University=20 of=20 Pernambuco          &nb= sp;           &nbs= p;     =20 Brazil
---------------------------------------------------------------= ----------------------------
------=_NextPart_000_0099_01BDBC6F.C39956C0-- From bersuker@ne059.cm.utexas.edu Fri Jul 31 10:25:06 1998 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA01458 Fri, 31 Jul 1998 10:25:05 -0400 (EDT) Received: from ne056.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA05181; Fri, 31 Jul 1998 09:23:37 -0500 Message-Id: <35C1D255.BD2482F3@eeyore.cm.utexas.edu> Date: Fri, 31 Jul 1998 09:19:01 -0500 From: "Isaac B. Bersuker" Organization: The University of Texas at Austin X-Mailer: Mozilla 4.04 [en] (WinNT; I) Mime-Version: 1.0 To: "Henry J. Castejon" Cc: CHEMISTRY@www.ccl.net Subject: Re: second and third row transition metals References: <9807291724.AA14932@kbw350.chem.yale.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Status: RO Content-Length: 1402 If you are interested in methods to do such calculations for large systems, have a look into our paper in Internat. J. Quant. Chem. 63 (1997) 1051, it may be useful. Bersuker Henry J. Castejon wrote: > Hello everyone: > > Can someone help me with the following: > > I want to do molecular orbital calculations on second and third > row transition metals. The compounds contain many more than one > metal atom. (four or five). Consequently, I'm looking for some > software capable of doing that. Gaussian doesn't have basis > set for such metals and it may be a software using plane wave > or something else. > > I will appreciate if someone can give a hint on this. > Ah! I forgot a minor detail if the software is free better. > Although I may be willing to spend some money on it. > > Thanks a lot for anything you can do. If I get a good compilation > of answers I will summarize for everybody. > > Henry. > From p_kane@mailcity.com Fri Jul 31 14:31:02 1998 Received: from mailcity.com (fes.whowhere.com [209.1.236.79]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA05132 Fri, 31 Jul 1998 14:31:01 -0400 (EDT) Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Fri Jul 31 11:30:24 1998 To: "sp" , "mmod" , "CCL" Date: Fri, 31 Jul 1998 11:30:24 -0700 From: "Paddy Kane" Message-ID: Mime-Version: 1.0 X-Sent-Mail: on X-Mailer: MailCity Service Subject: Monte Carlo: Request For Key Papers X-Sender-Ip: 136.206.1.19 Organization: MailCity (http://www.mailcity.com:80) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have been using Spartan and MacroModel to carry out Monte Carlo conformational searches. I am looking for key references for the Monte Carlo method, most importantly, those messages which explain the theory behind such searches. I will summarise the responses and send them to the list. Thank you in advance for your replies. Kind rgds, Paddy. --- Paddy Kane School Of Chemical Sciences Dublin City University Glasnevin Dublin 9 Ireland. E-mail: p_kane@mailcity.com Tel: 00-353-1-7045641 Fax: 00-353-1-7045503 Now MailCity offers forwarding so you can check your MailCity messages and other e-mail all in one place. Go to http://www.mailcity.com From parthi@pegasus.arc.nasa.gov Fri Jul 31 17:11:57 1998 Received: from pegasus.arc.nasa.gov (pegasus.arc.nasa.gov [128.102.199.140]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA06946 Fri, 31 Jul 1998 17:11:56 -0400 (EDT) Received: from localhost (parthi@localhost) by pegasus.arc.nasa.gov (8.8.7/8.8.5) with SMTP id OAA12975; Fri, 31 Jul 1998 14:08:53 -0700 (PDT) Date: Fri, 31 Jul 1998 14:08:53 -0700 (PDT) From: "S. Parthiban" To: castejon@kbw350.chem.yale.edu cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Re: second and third row transition metals In-Reply-To: <35C1D255.BD2482F3@eeyore.cm.utexas.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You can find the 6-31G* basis set for K through Zn (K, Ca, Sc, Ti, V, Cr Mn, Fe, Co, Ni, Cu, Zn) in the paper JCP vol.109, (4) 1223-1229, 1998. It is a 22 July 1998 issue. Hope this helps. Parthiban S > > Hello everyone: > > > > Can someone help me with the following: > > > > I want to do molecular orbital calculations on second and third > > row transition metals. The compounds contain many more than one > > metal atom. (four or five). Consequently, I'm looking for some > > software capable of doing that. Gaussian doesn't have basis > > set for such metals and it may be a software using plane wave > > or something else. > > > > I will appreciate if someone can give a hint on this. > > Ah! I forgot a minor detail if the software is free better. > > Although I may be willing to spend some money on it. > > > > Thanks a lot for anything you can do. If I get a good compilation > > of answers I will summarize for everybody. > > > > Henry. > > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > >