From luo@seas.marine.usf.edu Wed Mar 12 10:28:49 1997 Received: from seas.marine.usf.edu for luo@seas.marine.usf.edu by www.ccl.net (8.8.3/950822.1) id JAA02903; Wed, 12 Mar 1997 09:39:54 -0500 (EST) Received: from localhost (luo@localhost) by seas.marine.usf.edu (8.8.5/8.8.5) with SMTP id JAA07917 for ; Wed, 12 Mar 1997 09:40:39 -0500 (EST) Date: Wed, 12 Mar 1997 09:40:39 -0500 (EST) From: Yu-Ran Luo To: chemistry@www.ccl.net Subject: Which Company Has This Software? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Which company has this software? We are looking for calculation/draw structure software which are good for transition metals and lanthanide series. Which company has this software? Could you send all information to me? My address: Dr. Yu-Ran Luo, Department of Marine Science, University of Florida, 140 7th Av. South, St. Petersburg, Florida 33701. E-Mail: luo@seas.marine.usf.edu From mdoyle@msi.com Wed Mar 12 11:05:45 1997 Received: from nic.cerf.net for mdoyle@msi.com by www.ccl.net (8.8.3/950822.1) id KAA03207; Wed, 12 Mar 1997 10:21:06 -0500 (EST) Received: from mica.msi.com (mica.msi.com [146.202.6.217]) by nic.cerf.net (8.8.5/8.8.8) with SMTP id HAA17981 for ; Wed, 12 Mar 1997 07:21:05 -0800 (PST) Received: from by mica.msi.com (4.1/SMI-4.1) id AB18786; Wed, 12 Mar 97 07:25:55 PST Message-Id: <3.0.32.19970312092050.006b910c@146.202.6.217> X-Sender: mdoyle@146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 12 Mar 1997 09:21:36 -0600 To: chemistry@www.ccl.net From: Michael Doyle Subject: *** Molecular Simulations Positions *** Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, Firstly my thanks for allowing me to use som of you band width. Secondly I hope the following information may be of interest to some of the people reading this list. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= MOLECULAR SIMULATIONS ANNOUNCES THE CREATION OF NEW POSITIONS FOR CUSTOMER FIELD SCIENCE SUPPORT. Molecular Simulations Inc. (MSI) (www.msi.com) is the leading provider of simulation and consulting modelling products to companies and universities world wide. MSI has a wide and diverse customer base in the USA, Europe, Japan and the Asia-Pacific region. As a consequence of this there now exists a chance to join a skilled team of Phd scientist in the field operations of MSI in the USA. This team deals with the application of modelling methods by, consultation with, and training of customer(s). This team also works in transferring technology to and in the research and application of modelling methods in business and research problems. The team identifies the technical aspects of customer business problems and matches these with the available resources within MSI or performs the task itself. MSI field scientists also decide the technical approach to new opportunities and identifies applications in collaborative and contract research within the diverse customer base. MSI is seeking candidates with the highest caliber credentials (Phd and preferably 4 years post doctoral experience) for three positions within this expanded group. The ideal background of candidates is from one of the following fields, solid state quantum mechanics, molecular mechanics, polymer modelling and correlation or GFA modelling. MSI provides a stimulating and rewarding work place and is a dynamic and forward looking company. Please forward any enquiries to mkearnes@msi.com or mdoyle@msi.com =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-=-=-=-=- Michael Doyle @ MSI Applications Science Manager US-Materials WRK 281-364-8555 FAX 281-364-0210 VOX 281-775-9012 HME 281-363-0361 (VOX&FAX) CAR 281-386-5211 WEB www.msi.com -=-=-=-=-=-=-=-=-=-=-=- From SMILLER@RARUSRAEXS1.prius.jnj.com Wed Mar 12 11:28:51 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id KAA03416; Wed, 12 Mar 1997 10:47:57 -0500 (EST) Received: by smtp-internet.jnj.com id AA27548 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 12 Mar 1997 10:47:14 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Wed, 12 Mar 1997 10:47:14 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Wed, 12 Mar 1997 10:47:14 -0500 Date: Wed, 12 Mar 1997 10:49:14 -0500 From: "Miller, Susan [PRI]" Subject: QSAR - Followup, again To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Thanks again for all of your responses. I will post a summary in a couple of days when the discussion is over. All of the responses I've received so far have come to CCL and not to my personal mailbox, but if it is desired, I can still post a compilation of the responses. I forgot to mention 2 very important facts: 1) I am using SYBYL and have no access to anything else, save the free software on the net. I cannot use that however, for the second reason. 2) My mentor insists that I do the overlays by hand, that is, by using the fit module in SYBYL and picking points, with the mouse, to fit. I must also do torsion adjustments by hand, that is, by choosing a torsion angle for each bond and applying it, using either the twist widget in the upper left corner of the screen or the modify torsion command. Susan From chemtw@showme.missouri.edu Wed Mar 12 13:28:51 1997 Received: from mail.missouri.edu for chemtw@showme.missouri.edu by www.ccl.net (8.8.3/950822.1) id MAA04031; Wed, 12 Mar 1997 12:34:18 -0500 (EST) Received: from black.missouri.edu (black.missouri.edu [128.206.2.222]) by mail.missouri.edu (8.8.5/8.8.5) with ESMTP id LAA70714 for ; Wed, 12 Mar 1997 11:34:13 -0600 Received: from localhost (chemtw@localhost) by black.missouri.edu (8.8.5/8.8.5) with SMTP id LAA29550 for ; Wed, 12 Mar 1997 11:34:11 -0600 X-Authentication-Warning: black.missouri.edu: chemtw owned process doing -bs Date: Wed, 12 Mar 1997 11:34:11 -0600 (CST) From: Troy Wymore X-Sender: chemtw@black.missouri.edu To: chemistry@www.ccl.net Subject: g(r) using CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I am having one major problem making a radial distribution function using CHARMM24. It seems no matter what I do I get a bus error (core dumped) when running my script. My trajectory file is from a simulation involving about 5,000 atoms. I have reduced the number of frames to read when constructing the radial distribution function but this does not help. My script,after reading in the topology, parameter, psf, coordinate and image files looks as such: set nfil 32 set iun 21 label olp open unit @iun read file name box_subp2_dyn2f.trj.@nfil incr iun by 1 incr nfil by 1 if nfil le 34 goto olp traj iread 21 nread 3 skip 1000 begin 181500 stop 183500 ! THIS IS THE LOOP OVER FRAMES set nfrm 1 label lp1 traj read update inbfrq 1 imgfrq 1 cutim 13.0 cutnb 13.0 wmin 1.5 coor dist image sele resn TIP3 .and. type OH2 end sele segid - PEP .and. resn ARG .and. type NH1 end - cut 8.5 hist hmin 0.0 hmax 8. hnum 80 hsave incr nfrm by 1 if nfrm le 3 goto lp1 bomblev -3 open unit 10 write card name argnh-gr.dat ! HNORM IS 1 PEP x 3 FRAMES outu 10 coor dist image sele none end sele none end cut 8.5 hist - hmin 0.0 hmax 8. hnum 80 hsave hnorm 3. hprint outu 6 stop If not for the bus error, I think this script should work. But it never gets beyond looping over the frames and usually not that far. I know people have analyzed longer and larger trajectories than this so I must be doing something wrong. Any suggestions would be much appreciated. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** From maiden@RedBrick.DCU.IE Wed Mar 12 14:29:10 1997 Received: from tolka.dcu.ie for maiden@RedBrick.DCU.IE by www.ccl.net (8.8.3/950822.1) id OAA04594; Wed, 12 Mar 1997 14:02:38 -0500 (EST) Received: from Nurse.RedBrick.DCU.IE by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA22195; Wed, 12 Mar 1997 19:01:54 GMT Received: (from maiden@localhost) by RedBrick.DCU.IE (SomeMTA) id SAA04112; Wed, 12 Mar 1997 18:59:30 GMT Organisation: DCU Networking Society X-Disclaimer: The DCUNS is not responsible for the content of this message Date: Wed, 12 Mar 1997 18:59:30 +0000 (GMT) From: michael nolan To: youngd2@mail.auburn.edu Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Chem Topic: Excited States In-Reply-To: <199703071616.KAA03874@wood.mail.auburn.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > IMPOSING ORTHOGONALITY - DFT TECHNIQUES > > Traditionally, excited states have not been one of the strong > points of density functional theory. This is due to the difficulty > in ensuring orthogonality to the ground state wave function when > no wave functions are being used in the calculation. > > The easiest excited states to find using density functional > theory techniques are those which are the lowest state of a given > symmetry thus using a ground state calculation. > > A promising techniques is one which uses a variational bound > for the average of the first M states of a molecule. > > A few other options have been examined. However, there is not > yet a large enough volume of work applying DFT to excited states to > predict the reliability of any of these techniques. > The imp himself has spoken *************************************************************************************** Michael Nolan (nearly BSc.) Dublin City University (quantum chem.) 41 Woodview Chemistry + german Year 4 Lucan Co. Dublin Ireland / Republic of Ireland / ROI / Eire Email: Maiden@redbrick.dcu.ie **************************************************************************************** You might like to check out Goerling's method in phys rev A nov/dec 1996. >From chipot@host7.lctn.u-nancy.fr Tue Mar 11 05:52 EST 1997 Received: from host7.lctn.u-nancy.fr for chipot@host7.lctn.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id FAA22752; Tue, 11 Mar 1997 05:52:09 -0500 (EST) Received: (from chipot@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id LAA26996 for chemistry-request@www.ccl.net; Tue, 11 Mar 1997 11:53:05 +0100 (NFT) From: Message-Id: <199703111053.LAA26996@host7.lctn.u-nancy.fr> Subject: Re: CCL:Thermodynamic integration To: chemistry-request@www.ccl.net (Jonathan Arthur) Date: Tue, 11 Mar 1997 11:53:05 +0100 (NFT) In-Reply-To: from "Jonathan Arthur" at Mar 11, 97 02:27:36 pm X-Mailer: ELM [version 2.4 PL23] Hi, there: > I am trying to perform a molecular dynamics calculation of the free > energy for the mutation of a water molecule into a methane molecule > in solution. I am using the thermodynamic integration technique. > Although I have been trying for quite a while, gradually finding > the bugs in my code, I have still not been able to reproduce the > literature values for this reaction. > > I am starting to suspect that I may not have a correct understanding > of how this technique is used. While the many references I have > consulted talk of 'accumulating the partial derivative dU/dlambda' > they do not describe exactly what this partial derviative is in > terms of the positions, velocites etc that can be accumulated each > time step. First thing: what you want to calculate is: 1 delta G = integral < dU(x,lambda) / dlambda > dlambda 0 lambda In the simulation, the integrand comes from a discrete number of points and your integral is approximated via a standard rule, such as Simpson, or trapezoidal: N delta G ~ sum { < dU(x,lambda) / dlambda > + 0 lambda(k) < dU(x,lambda) / dlambda > } x lambda(k+1) { lambda(k+1) - lambda(k) } / 2 The choice of N, the number of windows, can be critical for `mutation'- type free energy calculation... My experience is that it is often more efficient to use few windows (say less than 30) with extensive sampling than the contrary. Be sure, though, that the integrand varies smoothly. Now, for that kind of simulation, I assume that you `grow' bonds, con- comittently with increasing van der Waals radii. This deserves particu- lar attention, especially if bonds are shaken. What you should evaluate here is the contribution to the free energy of the constraints changing the bond lengths from lambda = 0 to 1. Simply, the latter can be calcu- lated from: dUconstraint / dlambda = {(Fij . rij) / |rij|} x (drij / dlambda) where Fij is the force dur to the constraint and rij is the constrained bond length. One last, trivial thing. For the above mutation, I guess you decouple the process into subprocesses, dedicated to electrostatic and internal+ van der Waals parameters... It is always safer to do so, especially for `absolute' free energies, than mutating everything simultaneously - un- less species at lambda = 0 and 1 are topologically identical (say K+ -> Na+). Hope this helps... Chris _______________________________________________________________________ Chris Chipot Laboratoire de Chimie Theorique Phone: (33) 3-83-91-25-96 U.R.A. C.N.R.S. No 510 Fax: (33) 3-83-91-25-30 Universite Henri Poincare - Nancy I B.P. 239 54506 Vandoeuvre-les-Nancy Cedex E-mail: chipot@lctn.u-nancy.fr _______________________________________________________________________ From ahocquet@tamarugo.cec.uchile.cl Wed Mar 12 20:28:54 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id TAA06617; Wed, 12 Mar 1997 19:00:34 -0500 (EST) Received: from 146.83.10.50 ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA28802; Wed, 12 Mar 1997 20:59:46 +0400 Message-Id: <33271884.3448@cec.uchile.cl> Date: Wed, 12 Mar 1997 20:57:03 +0000 From: Alexandre Hocquet Reply-To: ahocquet@tamarugo.cec.uchile.cl Organization: Universidad de Chile X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: the MM2 (big) family Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CClers, I am currently attempting to make a census of the MM2 versions, those natural sons that are based upon, but not identical to (they are no clones) one of the official Allinger's MM2 = versions. Of course they are thousands if one counts as a new version a MM2 to which were added a few parameters. For the purposes of my inventory, i will define a *different* version, one that differs in : - the equations of the force field terms (stretch, Van der Waals...) - the definitions of the nonbonded terms (point charges for bonds dipoles) - the treatment of conjugation - evaluating parameters that are not defined - recognizing substructures - treatment of strucures with more than 4 bonds attached to an atom Taking (Gundertofte et al., J.Comput.Chem., 1996, p429) as a starting point, i can name : MM2*(Macromodel) : Mohamadi et al., J.Comput.Chem., 1990, p440 "MM2" (Chem3D) : no reference MMX (PC model) : Gajewski et al., Advances in Molecular Modeling, Liotta Ed, JAI Press, Greenwich, CT, 1990 **If someone has a reprint of this reference, i am highly interested** an MMP2 variant : Liljefors et al., J.Comput.Chem., 1985, p478 Furthermore i can quote : MM+ (Hyperchem) : no reference MM2X (Optimol) : Holloway et al., J.Med.Chem., 1995, p305 If you know others, please let me know. Also, if you know other criteria that could be pertinent to define a *different* version, do not hesitate either. I will of course summarize if sufficient interest. -- = Alexandre Hocquet Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro Chile fono : 56 2 678 45 19 fax : 56 2 696 73 59 email : ahocquet@cec.uchile.cl >From FR042008@YSUB.YSU.EDU Wed Mar 12 17:40 EST 1997 Received: from YSUB.YSU.EDU for FR042008@YSUB.YSU.EDU by bedrock.ccl.net (8.8.3/950822.1) id RAA01264; Wed, 12 Mar 1997 17:40:12 -0500 (EST) Received: from YSUB.YSU.EDU by YSUB.YSU.EDU (IBM VM SMTP V2R3) with BSMTP id 1570; Wed, 12 Mar 97 17:38:57 EST Received: from YSUB.YSU.EDU (NJE origin FR042008@YSUB) by YSUB.YSU.EDU (LMail V1.2c/1.8c) with RFC822 id 7137; Wed, 12 Mar 1997 17:38:58 -0500 Message-Id: <199703122240.RAA01264@bedrock.ccl.net> Date: Wed, 12 Mar 97 17:38:04 EST From: "Janet Del Bene" To: chemistry@www.ccl.net Subject: 97.07.10 Buckingham Conf (Opt/Elec/Magn. Properties of Molecules) OPTICAL, ELECTRIC AND MAGNETIC PROPERTIES OF MOLECULES: A conference to celebrate the career of Professor A. D. Buckingham July 10-13 1997 Cambridge, UK FINAL CIRCULAR AND REGISTRATION FORM Preliminary Programme: (subject to change) ========================================== Thursday July 10 1997 --------------------- 12.00 - 13.30 Lunch at Pembroke College 13.00 - 14.15 Registration at the Department of Chemistry 14.15 - 14:30 Opening Remarks: Prof Alec Broers, Vice Chancellor of Cambridge University 14.30 - 15.10 An outline of the career of David Buckingham: D. P. Craig (ANU, Australia) 15.10 - 15.55 Invited Keynote Lecture: D. R. Herschbach (Harvard, USA) 15.55 - 16.25 Afternoon Tea 16.25 - 17.10 Invited Keynote Lecture: A. H. Zewail (Caltech, USA) 17.10 - 17.40 D. M. Neumark (Berkeley, USA) 17.40 - 18.10 C. A. de Lange (Amsterdam, Netherlands) 18.30 Conference photograph 19.30 Dinner at Pembroke College 20.45 Reception in the Old Library, Pembroke College (Sponsored by Taylor and Francis) Friday July 11 1997 ------------------- 9.00 - 9.45 Invited Keynote Lecture: W. Klemperer (Harvard, USA) 9.45 - 10.15 R. J. Saykally (Berkeley, USA) 10.15 - 10.45 J. M. Hutson (Durham, UK) 10.45 - 11.10 Morning Tea 11.10 - 11.55 Invited Keynote Lecture: D. A. King (Cambridge, UK) 11.55 - 12.40 Invited Keynote Lecture: J.-P. Hansen (Lyon, France) 13.00 - 14.15 Lunch at Pembroke College Early afternoon free until: 16.30 - 18.30 Poster Session at Pembroke College (sponsored by Taylor and Francis) 19.30 Dinner at Pembroke College Saturday July 12 1997 --------------------- 9.00 - 9.45 Invited Keynote Lecture: J. A. Pople (Northwestern University, USA) 9.45 - 10.15 P. W. Fowler (Exeter, UK) 10.15 - 10.45 J.-L. Rivail (Nancy, France) 10.45 - 11.15 Morning Tea 11.15 - 12.00 Invited Keynote Lecture: R. A. Marcus (Caltech, USA) 12.00 - 12.30 G. L. D. Ritchie (UNE, Australia) 13.00 - 14.15 Lunch at Pembroke College 15.00 - 15.30 P. J. Stephens (UCLA, USA) 15.30 - 16.00 L. D. Barron (Glasgow, UK) 16.00 - 16.30 Afternoon Tea 16.30 - 17.15 Invited Keynote Lecture: N. C. Handy (Cambridge, UK) 19.00 Reception at Pembroke College 19.30 Conference Banquet at Pembroke College Sponsored by: ============= Elsevier Taylor & Francis Shell CCP6 ************************************************************* REGISTRATION FORM please email to the conference secretary mjtj2@cus.cam.ac.uk ************************************************************* OPTICAL, ELECTRIC AND MAGNETIC PROPERTIES OF MOLECULES: A conference to celebrate the career of Professor A. D. Buckingham July 10-13 1997 Cambridge, UK REGISTRATION FORM Name: ......................................................................... Affiliation: .................................................................. Address: ....................................................................... ....................................................................... ....................................................................... .................................................... Fax Number: .............................................................. Email Address: ................................................................. Dietary Restrictions: ....................................... Poster Title (optional): .................................... ....................................................................... Registration Category: Full Registration .........................240.00 PST ________ Partial Registration ......................160.00 PST _______ Accompanying Persons ......................115.00 PST _______ Extra night's accommodation, Wed July 9 ... 32.00 PST _______ Extra night's accommodation, Sun July 13 .. 32.00 PST _______ Late Registration Fee (after June 1) .......15.00 PST _______ ======= Total Payable: _______ Payment must be made by cheque, payable to "David Buckingham Conference" in UK pounds only, and sent to the conference secretary: Dr Meredith Jordan Conference Secretary Department of Chemistry University of Cambridge Lensfield Rd, CB2 1EW, UK Payment will be due within 30 days of email registration. *************************************************************