From chemistry-request@server.ccl.net Thu Jan 18 04:11:29 2001 Received: from rudjer.irb.hr (simek@rudjer.irb.hr [161.53.128.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0I9BTd07197 for ; Thu, 18 Jan 2001 04:11:29 -0500 Received: from localhost (simek@localhost) by rudjer.irb.hr (8.10.0/8.10.0VS) with ESMTP id f0I9BSi06218; Thu, 18 Jan 2001 10:11:28 +0100 (MET) Date: Thu, 18 Jan 2001 10:11:28 +0100 (MET) From: Visnja Stepanic Reply-To: Visnja Stepanic To: chemistry@ccl.net cc: Visnja Stepanic Subject: Binary complexes in gas phase Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, is there a H-bonded binary system for which both molecular and ionic forms in gas phase have been determined, either experimentally or computationally? Is that possible at all? I am very grateful for your help in advance, Visnja --------------------------------------------------- Visnja Stepanic Laboratory of Molecular Spectroscopy Rudjer Boskovic Institute P.O.B. 180, Zagreb, Croatia Tel:385-1-45-60-963 Fax:385-1-46-80-195 ---------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 18 04:55:10 2001 Received: from asp.biogeo.uw.edu.pl (IDENT:root@asp.biogeo.uw.edu.pl [212.87.8.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0I9t9d07334 for ; Thu, 18 Jan 2001 04:55:09 -0500 Received: (from grzesb@localhost) by asp.biogeo.uw.edu.pl (8.9.3/8.9.3) id KAA27570 for CHEMISTRY@ccl.net; Thu, 18 Jan 2001 10:55:28 +0100 Date: Thu, 18 Jan 2001 10:55:28 +0100 From: Grzegorz Bakalarski To: CHEMISTRY@ccl.net Subject: Summary: vdW parameters Message-ID: <20010118105528.A27457@asp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i Hello, About week ago I asked: > Recently I analyzed vdW parameters in different > force fields > (sybyl, few flavors from MSI, Charmm, MM3 etc) and I > noticed > that the parameters differ substantially! > In crystallografer community the most popular are > Bondi vdW radii > and they are in most cases completely different from > those used in forcefields. > The only exception is sybyl forcefield, but here > also parameter for > H atom is 1.5 A (instead of 1.2 A) which gives 0.6A > difference for H-H > interaction. > My question is: what is origin of these (huge) > differences ? Physical > origin of the vdW is known and should not change > from forcefield to > forcefield ... > In a case of overlapping H-H pair a repulsive force > calculated using > sybyl vdW radii is substantial, (e.g. if distance is > 2.5A) but using > Bondi's radii the force is small and even > attracting Here are responses I've got. Thanks again to all for valuable discussion. G.Bakalarski +++++++++++++++++++ *From: "Michael K. Gilson" The variation in H-bond radii may come in part from the fact that most current force-fields model hydrogen bonds in terms of electrostatics (Coulomb's law) + vdw interactions. In order to get a good strong H-bond, the radius of a polar H must be artificially reduced so the H's positive charge can get close to the H-bond acceptor. If you need a reference for this, let me know and I'll dig one up. Regards, Mike Gilson ++++++++++++++++++++ *From: Marvin Waldman With regard to your CCL question below about differences in vdW parameters, it has been found that the parameters can be quite sensitive to various factors such as the form of the potential function (e.g. exp-6, LJ 12-6, LJ 9-6, ...), the form of the combination rules used for mixed parameters, the charge model used, and most importantly, the type of data used to fit the parameters (e.g. crystal structures, liquid simulations, ...). Also, the parameters will be correlated with the torsional parameters of a force field as both are generally involved in determining vicinal (1-4) interactions. As such, the parameters indeed do tend to vary quite substantially. The vdW parameters are _not_ experimental_ observables. Rather, they are part of an overall model (the force field) which is used to predict/fit various experimental results. Depending on the particular types of experiment you are trying to predict/fit and the rest of the force field model, the vdW parameters themselves can be quite different. Discussion of some of these points can be found in the following references: Z.Peng, C.S. Ewig, M.-J. Hwang, M. Waldman, A.T. Hagler, J.Phys.Chem. A, vol. 101, pp. 7243-7252 (1997) C.S. Ewig, T.S. Thacher, A.T. Hagler, J.Phys.Chem. B, vol. 103, pp. 6998-7014 (1999) Regards, Marvin Waldman, Ph.D. Senior Director, Rational and Combinatorial Drug Design Molecular Simulations Inc. ++++++++++++++++++++++ *From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) --- You wrote: what is origin of these (huge) differences ? --- end of quote --- Your question is a good one. The answer turns out to be fairly simple, but it has several parts. First, the vdW parameters used by force fields (FF) are designed to reproduce geometries of +particular molecules selected by the FF developer. The identities of these molecules vary from one +developer to the next, so the target data is not the same for all FF. Also, one can think of a FF as having two parts, the vdW part and everything else. The "everything +else" part varies from one FF to the next, so even if two FF tried to reproduce the same molecular +geometries they would have to use different "vdW" parameters to get there. (What is more, different +FF often use different equations to model vdW interactions, so different kinds of parameters are +required for this reason.) It also needs to be recognized that most FF are not designed to reproduce the data that so-called +experimental vdW radii are based on. Most (but not all) FF try to reproduce the geometries of +isolated molecules. Experimental vdW radii come from a variety of sources, but they generally +reflect some type of intermolecular interaction, and these interactions may contain more than vdW +interactions. As a result, comparing experimental and FF vdW parameters (and energies) may be +nonsensical. I hope this helps. You might consult Allinger's book, "Molecular Mechanics", for a more detailed +explanation. -Alan +++++++++++++++ *From: Rick Venable One issue may be the exact meaning of the "radii"; CHARMM radii represent the minimum of a Leonard-Jones 6-12 potential, while other force fields (like Merck) may use a somewhat different interpretion, as well as additional terms. You really have to look at the underlying equations used to explictly compute the VDW energy, and not just the radii. Although the physical basis for VDW may be understood as a diffusive interaction of the electron clouds which may have some long range character, most force fields use a simple Morse or LJ curve to model this interaction, which is mostly a short range approximation of the real VDW forces. -- Rick Venable +++++++++++++++ *From: Irilenia Nobeli Dear Grzegorz, Force fields are commonly empirically fitted which means that the van der Waals parameters are allowed to vary until the value of some property(ies) that depends on them agrees with either experimental or ab initio results. Hence although these parameters are normally restricted to some "acceptable" values, the optimum fitted values are unlikely to be identical to what one would expect from Bondi radii, the most common reason for this being that they have to absorb other inaccuracies in the potential, e.g. approximations to the dispersion energy by R6 terms and neglect of other terms such as polarisation energy. Hope this helps. Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&(end forever) From chemistry-request@server.ccl.net Thu Jan 18 15:56:22 2001 Received: from mail.cc.kuleuven.ac.be (mail.cc.kuleuven.ac.be [134.58.10.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0IKuLd09923 for ; Thu, 18 Jan 2001 15:56:21 -0500 Received: from vsm85-an (tvd-10-67-116-212.tvd.kotnet.kuleuven.ac.be [10.67.116.212]) by mail.cc.kuleuven.ac.be (8.9.3/8.9.0) with SMTP id VAA153276 for ; Thu, 18 Jan 2001 21:56:21 +0100 Message-Id: <3.0.1.32.20010118220036.007c8100@mail.cc.kuleuven.ac.be> X-Sender: p1930275@mail.cc.kuleuven.ac.be X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Thu, 18 Jan 2001 22:00:36 +0100 To: chemistry@ccl.net From: An Depuydt Subject: Question about mopac150 and the GRAPH keyword Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, I downloaded mopac150 from a few different sites and I tried to do this several times but the program never seems to work with the GRAPH keyword, the error message is as follows and looks like a fortran bug: run-time error F6413: OPEN(*.zmt) - file already connected to a different unit Can anybody help me with this ? Thanks a lot ! An Depuydt From chemistry-request@server.ccl.net Thu Jan 18 16:31:51 2001 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0ILVpd10078 for ; Thu, 18 Jan 2001 16:31:51 -0500 Received: from glasgow.ks.uiuc.edu (glasgow.ks.uiuc.edu [130.126.120.45]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id PAA10464; Thu, 18 Jan 2001 15:31:51 -0600 (CST) Received: (from barryi@localhost) by glasgow.ks.uiuc.edu (8.9.3+Sun/8.9.1) id PAA08713; Thu, 18 Jan 2001 15:31:50 -0600 (CST) Date: Thu, 18 Jan 2001 15:31:50 -0600 From: Barry Isralewitz To: CHEMISTRY@ccl.net Cc: Sergei Tretiak Subject: Re: CCL:Polymer animations? Message-ID: <20010118153149.E8445@glasgow.ks.uiuc.edu> Mail-Followup-To: Barry Isralewitz , CHEMISTRY@ccl.net, Sergei Tretiak References: <2F18332777@citrine.indstate.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.7i In-Reply-To: ; from serg@markov.chem.rochester.edu on Fri, Jan 12, 2001 at 12:25:22PM -0500 Hi, Kevin wrote: > > > > simulation. I would like this information to make a movie of the > > > > polymer in action under this force field. Therefore, I'm looking for > > > > a simple, public-domain piece of software that I can feed these > > > > coordinates to, and will generate the corresponding graphics and play > > > > them back as a movie. One solution is VMD, free molecular visualization software... http://www.ks.uiuc.edu/Research/vmd/ The method of much movie making is: 1. Generate a series of numbered frames (e.g. movie-0001.tiff ... movie-0600.tiff) 2. Turn them into a single movie file for playback. In reverse order, Step 2: The easy part is step 2. A number of utilities turn numbered frames into movies. Some examples: ImageMagick convert (most UNIXes), mediaconvert (SGI), many Macintosh and Windows-based programs. Get ImageMagick 'convert' for free your Unix box at: http://www.imagemagick.org/ Note that animated gifs have limited colors (256) and often are displayed with programs (e.g. web browsers) that skip frames for a large file. An mpeg or quicktime movie makes more sense, and even reasonably large frame sizes play great on modern machines. Step 1: The harder (and occasionally more fun) part is step 1, making the frames. See the VMD script library: http://www.ks.uiuc.edu/Research/vmd/script_library/ or more specifically the trajectory/animation and 'movies' sections of the script library: http://www.ks.uiuc.edu/Research/vmd/script_library/categories/animation.html http://www.ks.uiuc.edu/Research/vmd/script_library/categories/movies.html A sample script is 'animatepdbs' http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/ For a look at some VMD animations (Quicktime format), see http://www.ks.uiuc.edu/Overview/movie_gallery/qt_movies/ Cheers, Barry -- Barry Isralewitz Beckman 3121 Theoretical Biophysics Group, UIUC Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Thu Jan 18 16:40:28 2001 Received: from sg17.chem.upenn.edu (SG17.CHEM.UPENN.EDU [130.91.65.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0ILeSd10119 for ; Thu, 18 Jan 2001 16:40:28 -0500 Received: from localhost (sanjoy@localhost) by sg17.chem.upenn.edu (8.9.2/8.9.2) with ESMTP id QAA33439 for ; Thu, 18 Jan 2001 16:40:29 -0500 (EST) Date: Thu, 18 Jan 2001 16:40:28 -0500 From: Sanjoy Bandyopadhyay To: chemistry@ccl.net Subject: Windows2000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I don't know whether this is the right platform to ask this question. I want to partition the disk in my computer (running Windows2000 in NTFS file system) to install RedHat Linux. Any help will be appreciated. Thanks. Sanjoy..