From fdeprof@is1.vub.ac.be Thu Dec 8 04:00:37 1994 Received: from rc1 for fdeprof@is1.vub.ac.be by www.ccl.net (8.6.9/930601.1506) id CAA05927; Thu, 8 Dec 1994 02:50:45 -0500 Received: from vnet3.vub.ac.be by rc1 (8.6.8.1/3.3.1 (Antoon Pardon)) id IAA02089; Thu, 8 Dec 1994 08:52:06 +0100 Received: from [134.184.22.207] (sterfpmc207) by vnet3.vub.ac.be (4.1/VUB.920213) id AA22162; Thu, 8 Dec 94 08:52:03 +0100 Date: Thu, 8 Dec 94 08:52:03 +0100 Message-Id: <9412080752.AA22162@vnet3.vub.ac.be> X-Sender: fdeprof@is1.vub.ac.be (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: fdeprof@is1.vub.ac.be Subject: Z matrix to cartesian coord. Hi All, I have a problem which is rather urgent. I have internal coordinates for a number of highly symmetric molecules (symmetry Ih). I would like to have the cartesian coordinates of these Z-matrices to a rather big accuracy (10-15 digits after the komma), to exchange with other people whose programs only read cartesian coordinates. Is there a possibility to obtain these cartesian coordinates to this larger accuracy with the Gaussian 92 program, in stead of the standard six digits after the komma the program yields ? Please mail all the answers to me as soon as possible, I will summarize for the net. Thanks, Frank De Proft From moret@far.ruu.nl Thu Dec 8 06:22:24 1994 Received: from accucx.cc.ruu.nl for moret@far.ruu.nl by www.ccl.net (8.6.9/930601.1506) id GAA07351; Thu, 8 Dec 1994 06:14:53 -0500 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by accucx.cc.ruu.nl with SMTP id AA06400 (5.65c/IDA-1.4.4 for ); Thu, 8 Dec 1994 12:14:51 +0100 Message-Id: <199412081114.AA06400@accucx.cc.ruu.nl> Received: by ruucmc.far.ruu.nl (16.6/16.2) id AA08177; Thu, 8 Dec 94 12:12:27 +0100 From: "E.E.Moret" Subject: Dendrimer modelling To: chemistry@ruucmc.far.ruu.nl Date: Thu, 8 Dec 94 12:12:27 MET Name: Ed Moret Organisation: Utrecht University Phone: 030 - 536979 Mailer: Elm [revision: 66.25] Dear colleagues, Dendrimers are branched polymers, resembling trees and branches, of an organic repeat unit. Several theories on their potential use have been proposed (for example Jansen et al., Science 18 november 1994, 1226-1229). Among other things, dendrimers might be of use as drug delivery systems. Their proposed structures, often visualised in 2D in the literature, are highly suggestive, but 3D information is scarce. We would like to study the influence of the conformation of the repeat-unit on the multiple-generation dendrimer that can be constructed. We are aware of software tools to polymerise repeat-units, especially the modules implemented in the commercial modelling packages. These modules, however, require ONE head and ONE tail atom to initiate polymerisation. Dendrimers, by definition, grow on 3 or more sites of the repeat unit. We would appreciate any suggestions on research performed in this area and on programs that can cope with this special kind of "molecular growth". Replies, if any, will be summarised for CCL. With best regards, Ed Moret ------------------------------------------------------------------------- E.E. Moret (@more@) E.E.Moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- From GDURST@ELINET1.DOWELANCO.COM Thu Dec 8 09:18:14 1994 Received: from ELINET1.DOWELANCO.COM for GDURST@ELINET1.DOWELANCO.COM by www.ccl.net (8.6.9/930601.1506) id IAA08459; Thu, 8 Dec 1994 08:20:25 -0500 Date: Thu, 8 Dec 1994 8:17:06 -0500 (EST) From: "Gregory L. Durst - DowElanco R&D" To: chemistry@ccl.net CC: GDURST@ELINET1.DOWELANCO.COM Message-Id: <941208081706.fd4d@ELINET1.DOWELANCO.COM> Subject: Superdelocalizability calcs? Hello Netters, I am interested in calculating superdelocalizability indexes >from MOPAC output. (I have an application where these may be useful in understanding a QSAR analysis). I was wondering if anyone out there has written a unix shell script or SPL script to do this. It appears this will be a *tedious* job otherwise. Searching the CCL archives turned up 2 other requests for similar calc's this past year, but no resopnses were recorded. Surely someone out there has looked at this before. Thanks in advance for any help, and I'll post a summary if there is interest. Regards, Greg +-----------------------------------------------------------------------+ | Gregory L. Durst Computational Chemistry | | phone: 317/337-3413 DowElanco R&D | | email: gdurst@dowelanco.com 9330 Zionsville Rd. Bldg 306/D2 | | Indianapolis, IN 46268 USA | +-----------------------------------------------------------------------+ From psubram@texaco.com Thu Dec 8 09:26:18 1994 Received: from texaco.com for psubram@texaco.com by www.ccl.net (8.6.9/930601.1506) id IAA08507; Thu, 8 Dec 1994 08:26:33 -0500 Received: by texaco.com (4.1/SMI-4.1) id AA25802; Thu, 8 Dec 94 07:25:59 CST Date: Thu, 8 Dec 94 07:25:59 CST From: psubram@texaco.com (Palavo Subramanian) Message-Id: <9412081325.AA25802@texaco.com> To: chemistry@ccl.net Subject: Polymer Chain Rigidity Dear Netters, I had posted a query on polymer rigidity a while back. Here is a summary of all the replies that I received. My sincere thanks to everyone who t took time to reply. : Return-Path: Received: from nickel.laurentian.ca by texaco.com (4.1/SMI-4.1) id AA29296; Thu, 1 Dec 94 15:23:28 CST Received: from NICKEL.LAURENTIAN.CA by NICKEL.LAURENTIAN.CA (PMDF V4.3-7 #7390) id <01HK4W0LIJ749KNBPA@NICKEL.LAURENTIAN.CA>; Thu, 1 Dec 1994 16:21:47 EST Date: Thu, 01 Dec 1994 16:21:47 -0500 (EST) From: GUSTAVO@nickel.laurentian.ca Subject: Re.: Quantifying polymer rigidity. Dear P. Subramanian, Regarding the measurement of rigidity in polymers, yes, as far as I know, the persistence length is the standard one-parameter descriptor used to that effect. Any other measure of angular autocorrelation along the chain will work similarly. I have developed an alternative measure of flexibility (or rigidity) that conveys also the shape of the polymer. This aspect is somewhat lost in the persistence length. The basic ideas and some applications of this approach are in: Phys.Rev. E 49 (1994) 2417 and J.Phys.Chem. 97 (1993) 13831. Other authors have proposed alternative characterizations of entanglements which could also be used to describe rigidity. Perhaps you may find these descriptors useful. Best regards, G. Arteca Dept. de Chimie et Biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6. ---------------------------------------------------------------------------- Return-Path: Received: from rose.chem.wesleyan.edu by texaco.com (4.1/SMI-4.1) id AA01879; Thu, 1 Dec 94 16:43:49 CST Received: from jellyfish.chem.wesleyan.edu by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA15195; Thu, 1 Dec 1994 17:37:47 -0500 Received: by jellyfish.chem.wesleyan.edu (NX5.67d/NX3.0S) id AA03411; Thu, 1 Dec 94 17:43:44 -0500 Date: Thu, 1 Dec 94 17:43:44 -0500 From: S. Vijayakumar Mani: Here is my 2 cents worth! Ideally, the lower the internal degrees of freedom the more rigid a molecule is. The predominant contributor to this would of course be rotations along the torsional angles. Crudely, one can assume that the flexibility of a polymer is directly proportional to the number of accessible states and inversely proportional to the conformational barrier between these states. For the former, you can perform a global conformational search and look at the number of accessible states (minimum energy conformations) within a fixed energy (usually about 5 Kcal) window. But the latter problem of estimating the barrier for conformational transition can be a bit more tricky and involved. In any case, you cannot consider the effects of temperature on the flexibility using this approach. A more easier approach, would be run an MC simulation of the polymer in vacuo or appropriate conditions at a series of temperatures and generate an ensemble of structure at each temperature. One can then think of ways to cluster these into groups of related conformations and figure out a composite index to estimate the flexibility based on the number of distinct states and the probability density at each state. On a general basis, persistence length is really only one of many criteria for estimating the flexibility. However, if the polymers that you are interested in is unbranched then it might suffice and could serve as an useful practical measure. Regards, Vijay ************************************************************* S. Vijayakumar, Ph. D., DCA Department of Chemistry, Wesleyan University, Middletown, CT 06459 Voice: (203) 685-2777 Fax: (203) 685-2211 email: vijay@rose.chem.wesleyan.edu ************************************************************* Return-Path: Received: from alpha.xerox.com by texaco.com (4.1/SMI-4.1) id AA24166; Fri, 2 Dec 94 07:55:41 CST Received: from XRCC_Mail.XRCC.XEROX.xns by alpha.xerox.com via XNS id <14460(8)>; Fri, 2 Dec 1994 05:55:28 PST X-Ns-Transport-Id: 080037006B5D3453328F Date: Fri, 2 Dec 1994 05:55:12 PST From: Sundar_Sundararajan.XRCC@xerox.com Subject: Chain rigidity Dear subramanian, concerning your question on calculating the chain rigidity : I have been using the conformational entropy as a numeric measure. I have related the chain rigidity, via calculated entropy, to functional properties such as the glass transition temperature (see Macromolecules, v. 26, 1993, p. 344. Sometimes, partition fucntions can be sued as well (Polym. Mater. Sci. Eng., v 63, 1990, p 392.) Regards Sundararajan sundar.xrcc@xerox.com ---------------------------------------------------------------------------- Return-Path: Received: from monte.br.rohmhaas.com by texaco.com (4.1/SMI-4.1) id AA25761; Fri, 2 Dec 94 08:40:20 CST Received: by monte.br.rohmhaas.com (AIX 3.2/UCB 5.64/4.03) id AA29638; Fri, 2 Dec 1994 09:33:45 -0500 From: rs0thp@rohmhaas.com (Dr. Tom Pierce) A good way to quantify rigidity depends on what you will experimentally measure as 'rigid'. The most compelling measures correlate with experiments. Interesting measures are: Radius of Gyration Variance of Radius of Gyration End-to-end distances Variance of end-to-end distances Characteristic ratio (Cinfinity) Kuhn segment (or Persistence Length) These are single chain estimates, returning to what does rigid mean, if you are interested in packing effects then volume calculations might be useful. Note that the relationship of Radius of Gyration to End-to_end distance will tell you "how" gaussian your chains are. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." --------------------------------------------------------------------------- Return-Path: From: burkhart@goodyear.com (Craig W. Burkhart) Subject: Chain Stiffness Mani, One of the most general ways to infer chain rigidity is calculation of the characteristic ratio. It is defined, for a simple linear chain, as C(n) = /nl^2 where s = chain end-to-end distance n = number of bonds along backbone l = bond distance The use of <> brackets implies an ensemble average. For a freely jointed chain, C(n) = 1. For a jointed chain with a bond angle of 120 degrees, C(n) ~ 2.5 or so. For polyethylene, C(n) = 6.6-6.9. This implies that polyethylene is fairly stiff compared to ideal chains. Main-chain liquid crystal polymers have C(n) > 10 (usually). So now you have an idea of how chain stiffness can be measured in this fashion. If you choose to do this via simulation, you BETTER BE SURE that your forcefield reproduces the conformational states of the chain extremely well. An RIS dyad analysis of the chain torsional states is probably the best route. Most of this information can be found in Flory's classic "Chain Statistics of Macromolecules". It is MUST reading for anyone who deals with polymer chain conformations and configuration statistics... You have mentioned persistence length. In order to obtain the persistence length, you have to do the same gyrations (pardon the pun) as with characteristic ratio. Both methods are complementary... Have fun! Craig -- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] | Papernet: Craig W. Burkhart | "One man's analytical is Goodyear Research | another man's numerical..." 142 Goodyear Blvd | Akron, OH 44305 | - old hacker's maxim Mouthnet: 216.796.3163 | Faxnet: .3304 | Internet: cburkhart@goodyear.com | [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Return-Path: From: "Bruce E. Wilson" Subject: Re: CCL:Polymer Chain Rigidity If you have a set of decent probabilities (and they can be calculated) a Rotational Isomeric State model to calculate end to end distances for an ensemble of molecules can be done very quickly. I've tended to divide by the end to end distance for a fully extended chain (which is not the same thing as topological length) or by the mass to get some sense of normalization. If the polymers are "reasonably" similar, you can just use the end to end distances for the same Mn and get reasonable results. If you don't have an RIS model, then the average end to end distance for a collection of three or four starting points during molecular dynamics (I prefer MM2, MM3) can work, although you'll probably want fairly long run times (hundreds of picoseconds). The RIS calcs can be done in a day easily, if you have decent probabilities. The MD calcs on most RS/6000 workstations may take a couple of weeks to get decent convergence. Bruce E. Wilson (bewilson@emn.com) Eastman Chemical Company -------------------------------------------------------------------------- Return-Path: From: dodd@roebling.poly.edu (Lawrence R. Dodd) Subject: Re: CCL:Polymer Chain Rigidity ::: "TP" == Tom Pierce writes: TP> Previously, Palavo Subramanian wrote: >> What is a good way to 'quantify' polymer chain rigidity ?. I am >> looking at comparing the rigidity of Polymer A as a function of >> temperature and also as a function of composition(monomer ratio >> in the case of a copolymer). Is there a good way to calculate >> this? Is Persistence Length a good measure of the rigidity? TP> These are single chain estimates, returning to what does rigid TP> mean, if you are interested in packing effects then volume TP> calculations might be useful. I don't know what volume type of calculations to which Tom refers, but we (Doros Theodorou and I) found that the molecular volume of (united atom) polymer chains was relatively independent of chain conformation and that the volume of an "all-trans" chain was as good as any other (Mol. Phys., 72(6), 1313-1345). --Mani-- From pesquer@lpct.u-bordeaux.fr Thu Dec 8 10:19:08 1994 Received: from ausone.lpct.u-bordeaux.fr for pesquer@lpct.u-bordeaux.fr by www.ccl.net (8.6.9/930601.1506) id JAA09934; Thu, 8 Dec 1994 09:54:59 -0500 From: Message-Id: <199412081454.JAA09934@www.ccl.net> Received: from mac4.lpct.u-bordeaux.fr by ausone.lpct.u-bordeaux.fr with SMTP (1.38.193.4/16.2) id AA01322; Thu, 8 Dec 1994 15:55:20 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: Eudora F1.4.2 Date: Thu, 8 Dec 1994 16:01:24 +0000 To: chemistry@ccl.net Subject: calculations of dipole moment derivative The analysis of IR spectra of isolated CH stretching vibration, in molecules like CHD2X (X being a very polarisable group), shows that the dipole moment derivative d(mu)/dq (q= CH stretching coordinate), is no longer colinear to the stretched bond. It seems quite probable that this rotation of the dipole change vector away from the direction of displacement, may be because the motion of the H atom charge induces a dipole in the polarizable group, so that the resultant dipole change vector rotates. We want to calculate the induced and resultant dipoles. Is it possible by ab-initio calculations, using GAUSSIAN 92 program? Thank you for your answers. **************************************************** * * Michel PESQUER E-Mail: pesquer@lpct.u-bordeaux.fr * **************************************************** * Labo: Physicochimie theorique. - U.B.I. - 33405 Talence Cedex * * Tel 56 84 63 12 Fax 56 84 66 45 **************************************************** * Delegation Regionale du CNRS. - B.P.105 - 33402 Talence Cedex * * Tel 56 37 80 80 Fax 57 96 10 56 * *************************************************** From monge@anny.psgvb.com Thu Dec 8 12:20:46 1994 Received: from anny.psgvb.com for monge@anny.psgvb.com by www.ccl.net (8.6.9/930601.1506) id LAA11562; Thu, 8 Dec 1994 11:40:42 -0500 Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA04450; Thu, 8 Dec 94 08:40:37 -0800 Date: Thu, 8 Dec 94 08:40:37 -0800 From: monge@anny.psgvb.com (Alessandro Monge) Message-Id: <9412081640.AA04450@anny.psgvb.com> To: chemistry@ccl.net Subject: Experimental data on solvation of big molecules Hi All: Does anybody have references to experimental work on solvation of big molecules (where big is 20 atoms or more)? If there is interest I can post a summary to the list. Thanks, Alessandro ------------------------------------------------------------------------ Alessandro Monge Schrodinger, Inc. monge@psgvb.com (800) 20-PSGVB From WAGENER@ps1515.chemie.uni-marburg.de Thu Dec 8 12:52:07 1994 Received: from Mailer.Uni-Marburg.DE for WAGENER@ps1515.chemie.uni-marburg.de by www.ccl.net (8.6.9/930601.1506) id MAA12418; Thu, 8 Dec 1994 12:16:05 -0500 Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA159050; Thu, 8 Dec 1994 18:16:17 +0100 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.13); Thu, 8 Dec 94 18:17:42 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.13); Thu, 8 Dec 94 18:17:29 GMT+2 To: chemistry@ccl.net From: "Thomas Wagener" Date: Thu, 8 Dec 1994 18:17:19 MDT Subject: f-type pol. functions for tin Reply-To: wagenert@Mailer.Uni-Marburg.DE Priority: normal X-Mailer: WinPMail v1.0 (R1) Message-Id: <9EF66CB16CF@ps1515.chemie.uni-marburg.de> Dear netters, can anyone tell me where I could find a basis set for tin that uses optimized f-type polarization functions. Any reference - literature, ftp-site or just an e-mail adress of someone I could ask - would be greatly apreciated. Thanks in advance, Thomas - "You are wrong! 2+2=5.9863! Please adjust your equipment accordingly" The Computer (your friend) From thys@schs.uia.ac.be Thu Dec 8 13:02:55 1994 Received: from sch2.uia.ac.be for thys@schs.uia.ac.be by www.ccl.net (8.6.9/930601.1506) id LAA11100; Thu, 8 Dec 1994 11:21:04 -0500 Received: from localhost by sch2.uia.ac.be (8.6.4/Ultrix3.0-C) id RAA23655; Thu, 8 Dec 1994 17:17:19 +0100 Date: Thu, 8 Dec 1994 17:17:10 +0100 (MET) From: Gerd Thys To: CCL Subject: Inverse laplacian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, My collegue is looking for a program to calculate the inverse laplacian of a function. Best regards Gerd ---------------------------------------------------------------------------- Gerd Thys Ph.D. Student Structural Chemistry Group University of Antwerp (UIA) Universiteitsplein 1 E-mail: thys@uia.ua.ac.be B-2610 wilrijk URL: http://www.uia.ac.be/u/thys/index.html BELGIUM ---------------------------------------------------------------------------- From djh@ccl.net Thu Dec 8 13:14:23 1994 Received: from xipe.ccl.net for djh@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA11300; Thu, 8 Dec 1994 11:27:18 -0500 From: David Heisterberg Received: for djh@ccl.net by xipe.ccl.net (8.6.9/920428.1525) id LAA01270; Thu, 8 Dec 1994 11:27:16 -0500 Date: Thu, 8 Dec 1994 11:27:16 -0500 Message-Id: <199412081627.LAA01270@xipe.ccl.net> To: chemistry@ccl.net Subject: Open shell singlets follow-up Content-Length: 955 I posted a question recently about problems running open shell singlets in Gamess using GVB. Nikita Matsunaga of Iowa State suggested doing the same calculation via MCSCF. That's something I'll be doing later, but for now I'd still like a Fock matrix approach. To that end I've found that Cadpac has an excellent and easy-to-use Generalized SCF. For a particular system I'm interested in, Mo2- (formate)4 complex, the 1A1g RHF run with 156 basis functions took 59 seconds on our Cray, the 1A2u open shell singlet run, starting with the RHF orbitals, took 438 seconds. Cadpac's GRHF also handles 2E states very well, starting from the appropriate cation or anion orbitals. Analytic 1st and 2nd derivatives are available for GRHF. -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) From mwd@alamos.cray.com Thu Dec 8 14:18:49 1994 Received: from timbuk.cray.com for mwd@alamos.cray.com by www.ccl.net (8.6.9/930601.1506) id NAA13958; Thu, 8 Dec 1994 13:44:47 -0500 Received: from pajarito.cray.com (mwd@pajarito.cray.com [128.162.56.9]) by timbuk.cray.com (8.6.9/8.6.9M) with SMTP id MAA07915 for ; Thu, 8 Dec 1994 12:44:43 -0600 Received: by pajarito.cray.com (5.0/CRI-5.13) id AA02207; Thu, 8 Dec 1994 11:44:39 +0700 From: mwd@alamos.cray.com (Mark Dalton) Message-Id: <9412081844.AA02207@pajarito.cray.com> Subject: Summary: Phospholipid 3d structure and forces To: chemistry@ccl.net Date: Thu, 8 Dec 1994 11:44:37 -0700 (MST) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 7758 Hi! Here is what I have heard/found about Phospholipids 3d structures and forces/characteristics (which I need find values for each characteristic of membrance components). The idea is to model a Cell (to be freely available for non-profit research). (Also I am working on writing a Virtual Cell Bio. Course that will be available via WWW/Mosaic - I need images still, clickable biology). I hope this can be of help to others also. Thanks! Mark Original Post: Subject: CCL:Phospholipid 3d structure and forces Date: Tue, 29 Nov 1994 17:19:16 -0600 (CST) Hi! I was wondering if anyone has suggestions or know of places where I could get 3D structures (PDB format) of (cell membrane) phospholipids, also if there are any formulas/information on strengths and rate of decrease of the hydrophilic/phobic interactions, pH and ionic strength of various phospholipids, proteins. Basically, I am looking for good, accurate and complete information of characteristics/properties of the various parts of cell membranes. Does anyone have good references? ---------------------< End of message >------------------------------ Just so it is clear, I am doing this on my own time, i.e. it is not part of my job. So Cray is not responsible for my actions,comments, or ideas. Of course the Biochem. and Cell Bio. textbooks. Here is what I have found (in the Cray Channels Volume 16, Number 1): Terry Stouch's work: 1. Stouch, Terry R., "Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers" Molecular Simulations, Vol. 10, No 2-3. pp. 317-345. 2. Stouch, Terry R., Howard E. Alper and Donna Bassolino, "Supercomputing Studies of Biomembranes" International Journal of Supercomputer Appllications, 1993. 3. Alper, Howard E., Donna Bassolino, and Terry R. Stouch, "Computer Simulations of a Phospholipid Monolayer-Water System: The influence of Long Range Forces on Water Structure and Dynamics" Journal of Chemical Physics, Vol 98, No. 12, pp. 9798-98-7, 1993. 4. Alper, Howard E., Donna Bassolino, and Terry R. Stouch, "The Limiting Behavior of Water Hydrating a Phospholipid Monolayer: A Computer Simulation Study," Journal of Chemical Physics, Vol. 99, No. 7, pp. 5547-5559, 1993. 5. Stouch, Terry R., Keith B. Ward, Amanda Altieri, Arnold T. Hagler, "Simulation of Lipid Crystals: Characterization of Potential Energy Functions and Parameters for Lecithin Molecules," Journal of Computational Chemistry, Vol. 12, No. 8, pp. 1033-1046, 1991. 6. Stouch, Terry R. and Donald E. Williams, "On the Conformational Derived Charges: Studies of the Fitting Procedure," Journal of Computational Chemistry, Vol. 14, No. 7, pp. 858-866, 1993. 7. Liang, Congxin, Carl S. Ewig, Terry R. Stouch, and Arnold T. Hagler, "Ab Initio Studies of Lipid Model Species. 1. Dimethylphosphate and Methylpropylphosphate Anions," Journal of American Chemical Society, Vol. 115, No. 4, pp. 1537-1545, 1993. 8. Stouch, Terry R. and Donald E. Williams, "Conformational Dependence of Electrostatic Potential Derived Charges of a Lipid Headgroup: Glycerylphosporylcholine," Journal of Computational Chemistry, Vol. 13, No. 5, pp. 622-632, 1992. 9. Williams, Donald E. and Terry R. Stouch, "Characterization of Force Fields for Lipid Molecules: Applications to Crystal Structures," Journal of Computational Chemistry, Vol. 14, No. 8, 1993. 10. Bassolino, Donna, Howard E. Alper, and Terry R. Stouch, "Solute Diffusion in Lipid Bilayer Membranes: An Atomic Level Study by Molecular Dynamics Simulation," Biochemistry, Nov. 30, 1993. Responses: 1. From mchee@oxmol.com Wed Nov 30 08:53:54 1994: Oxford Molecular has a package called Iditis which validates the PDB files from BrookHaven and derives additional properties for each protein (from macromolecular to atom level information). Thus, users will be able to obtain all sequence and structurel related information about any protein in the database. Anyway, in the latest release of the data, which corresponds to the April 1994 release of Brookhaven, there are 4 entries of the same phospholipid protein - 1AIN (Annexin I from Human), 1ALA (Annexin V from chicken), 1AVH (Annexin V Hexagonal crystal), 1AVR(Annexin V Rhombohedral crystal). The last two are from human placenta. All are Ca-binding. If you are interested in getting more information about Iditis, please contact the number below. Regards, Merk-Na ------------------------------------- Merk Na Chee, Ph.D. Applications and Support Oxford Molecular Inc. Springfield, VA 22151 E-mail: mchee@oxmol.com (Merk Na Chee) ------------------------------------- 2. From DCAMPER@elinet1.dowelanco.com Wed Nov 30 06:31:29 1994 Subject: lipids I don't have any specific reference at hand but I know Terry Stouch at Bristol Meyers Squib was involved in extensive modeling of lipid bylayers and I believe molecules within these lipids. This may be a place to start. Debby Camper dcamper@dowelanco.com 3. From ccevc16@pinar1.csic.es Wed Nov 30 02:38:08 1994 From: Victor Cruz Subject: Phospholipids You can find geometrical information at the Cambridge Crystallographic Database. In particular I am working with DLPE (dilauroil-phosphatidyl-choline) crystal structure taken from: Hitchcock,P.B.,et al.,Proc. Nat. Acad Sci. 71:3036(1974). Cambridge Database can be get from: Dr. Olga Kennard CCDC,University Chemical Laboratory,Lensfield Road,Cambridge CB2 1EW,U.K. 4. From newhoir@duc.auburn.edu Tue Nov 29 18:03:54 1994 From: newhoir@duc.auburn.edu (Irene Newhouse) Subject: Re: CCL:Phospholipid 3d structure and forces There's a big review on phospholipid structures by Irmin Pascher in Biochimica et Biophysica Acta that came out at the end of 1992; vol 1113, pp 339-73. Irene Newhouse 5. From wchutt@alex.monsanto.com Thu Dec 1 15:02:15 1994 From: wchutt@alex.monsanto.com (Bill C Hutton) Subject: phospholipds The only 3D data I know of is an old X-ray structure. I do not have the referene here, but I could bring it in. This is a very well known paper and is used in all of the monographs and reviews of phospholipid membranes. Some simulation work (computational chemistry) has been done as well. Also, I have dozens of non-propriatary NMR NOESY spectra of phospholpipd vesicles. No one really understands some of the featurews in this data. Modeling could really help out. This data could go a long way towards understanding curved bilayer structure and dynamics. I have not had the time or incentive to carefully evaluate all of the data. But is is quite interesting. Some early work can be found in J. Amer. Chem. Soc. 1985, 107 pp 1530-37. There are later papers as well but again I do not have the references here. ********************************************************************** W.C. Hutton, Monsanto Company, Corporate Research wchutt@monsanto.com This message does not necessarily reflect the views of Monsanto Company or, now that I think of it, anyone else. ********************************************************************** -- Mark Dalton CH3-S-CH2 H H O H Cray Research,Inc. | | | \ | Los Alamos,NM 87544 CH2-C-COOH //\ ---C--CH2-C-COO C-CH2-C-COO mwd@cray.com | | || || | // | NH2 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html From JAMES@unca.edu Thu Dec 8 15:18:29 1994 Received: from uncavx.unca.edu for JAMES@unca.edu by www.ccl.net (8.6.9/930601.1506) id OAA14675; Thu, 8 Dec 1994 14:27:46 -0500 Received: from uncavx.unca.edu by uncavx.unca.edu (PMDF V4.3-8 #5911) id <01HKEIFDSG3K051479@uncavx.unca.edu>; Thu, 8 Dec 1994 14:27:18 EST Date: Thu, 08 Dec 1994 14:27:17 -0500 (EST) From: "Charles G. James" Subject: Z matrix to cartesian coord. Question To: chemistry@ccl.net Message-id: <01HKEIFDUL9E051479@uncavx.unca.edu> Organization: University of North Carolina at Asheville X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I do not mean this as an attack upon anyone or anything. However this relates to information I have to pass on to undergraduates in reference to computational chemistry. Just this week someone on this mailing list asked for a way to get 10-15 (significant?) digits, after the komma(decimal), Cartesian coordinates for a Ih symmetry molecule from the z matrix of a Gaussian 92 program. Are we at the stage where that many significant digits are given by any computational chemistry method? Are we at the stage where that many significant digits are obtainable by any physical method used to measure structure? I am still warning undergraduates to beware of the number of digits which can appear in calculations not connected to their measurements or their original input. Can I now say there are ways out there to get precision only formerly dreamed by spectroscopist? Are there ways to get structural parameters to this precision? Charles G. James, Jr. Assoc. Professor of Chemistry Dept. of Chemistry, University of North Carolina at Asheville Asheville, NC 28804-3299, USA Phone: (704)251-6443 FAX: (704)251-6041 E-mail: james@unca.edu From bartberg@qtp.ufl.edu Thu Dec 8 16:18:33 1994 Received: from crunch for bartberg@qtp.ufl.edu by www.ccl.net (8.6.9/930601.1506) id PAA16211; Thu, 8 Dec 1994 15:44:24 -0500 Received: by crunch (5.x/4.11) id AA26608; Thu, 8 Dec 1994 15:44:22 -0500 Date: Thu, 8 Dec 1994 15:44:22 -0500 From: "Micheal Bartberger" Message-Id: <9412082044.AA26608@crunch> To: chemistry@ccl.net Subject: graphics programs Hello all. If this question has been asked in the past, please pardon the redundancy. I am interested in the availability of software packages for displaying geometries (such as the typical pictures of calculated or X-ray structures found in journal articles) along with the associated geometric data (bond distances, etc.) The ability to read various types of input files (XYZ, Internal, etc) would be fantastic. I'd like to find something decent to use in conjunction with a Windows-based word processor allowing the typical cut & paste functions, that is of publication quality. I'd imagine that there are of plenty of programs out there that will do a great job of this, but I haven't seen anything around the department. The displaying of bond distances, etc. does not have to be automatic (such as something like the CAChe Molecule Editor can do) but rather I am just looking for something that will give professional- looking structures for incorporation into an MS Word / WP / etc. document. These do not have to be public domain, and I will, of course, summarize if there is sufficient interest. Thanks! Michael D. Bartberger Department of Chemistry University of Florida bartberg@qtp.ufl.edu bartberg@chem.ufl.edu From laidig@pg.com Thu Dec 8 17:18:20 1994 Received: from oldspice.pg.com for laidig@pg.com by www.ccl.net (8.6.9/930601.1506) id RAA17949; Thu, 8 Dec 1994 17:12:44 -0500 Received: by oldspice.pg.com (8.6.9/8.6.9) id RAA23627; Thu, 8 Dec 1994 17:07:34 -0500 id RAA23627; Thu, 8 Dec 1994 17:07:34 -0500 Received: from pandora.pg.com(137.176.2.4) by oldspice.pg.com via smap (V1.3) id sma023621; Thu Dec 8 22:07:15 1994 Received: from morpheus.pg.com by pandora via SMTP (940715.SGI.52/930416.SGI.AUTO) for @oldspice.pg.com:JAMES@unca.edu id AA09430; Thu, 8 Dec 94 17:15:10 -0500 Received: by morpheus (931110.SGI/930416.SGI.AUTO) for @pandora.pg.com:chemistry@ccl.net id AA15817; Thu, 8 Dec 94 17:15:10 -0500 Date: Thu, 8 Dec 94 17:15:10 -0500 From: laidig@pg.com (Bill Laidig) Message-Id: <9412081715.ZM15815@morpheus.pg.com> In-Reply-To: "Charles G. James" "CCL:Z matrix to cartesian coord. Question" (Dec 8, 2:27pm) References: <01HKEIFDUL9E051479@uncavx.unca.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Charles G. James" , chemistry@ccl.net Subject: Re: CCL:Z matrix to cartesian coord. Question Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Dec 8, 2:27pm, Charles G. James wrote: > Subject: CCL:Z matrix to cartesian coord. Question > I do not mean this as an attack upon anyone or anything. However this relates > to information I have to pass on to undergraduates in reference to > computational chemistry. Just this week someone on this mailing list asked for > a way to get 10-15 (significant?) digits, after the komma(decimal), Cartesian > coordinates for a Ih symmetry molecule from the z matrix of a Gaussian > 92 program. Are we at the stage where that many significant digits are given by > any computational chemistry method? Are we at the stage where that many > significant digits are obtainable by any physical method used to measure > structure? I am still warning undergraduates to beware of the number of digits > which can appear in calculations not connected to their measurements or their > original input. Can I now say there are ways out there to get precision only > formerly dreamed by spectroscopist? Are there ways to get structural parameters > to this precision? > > Charles G. James, Jr. Assoc. Professor of Chemistry > Dept. of Chemistry, University of North Carolina at Asheville > Asheville, NC 28804-3299, USA Phone: (704)251-6443 > FAX: (704)251-6041 E-mail: james@unca.edu Prof. James, I believe you misunderstood the intent of the message you referred to. The author wanted his high symmetry geometry to be converted from internal to cartesian coordinates to 10-15 digit accuracy. The reason for this is not that the structures are assumed to be good to this many decimal places, but that programs that figure out symmetry from cartesian coordinates very often need the symmetry exactly or nearly exactly before there are able to pick it up. My interpretation is the standard 6 decimal places he has from his g92 output file is not accurate enough for the program he is subsequently using for it determine or to verify that the molecule really is Ih symmetry. Bill -- ****************************************************************************** * "Like jewels in a crown, the precious stones glittered in the queen's * * round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidigwd@pg.com * * Cincinnati, OH 45253-8707 laidig@qtp.ufl.edu * ****************************************************************************** From tripos!metis!matt@uunet.uu.net Thu Dec 8 19:18:21 1994 Received: from relay1.UU.NET for tripos!metis!matt@uunet.uu.net by www.ccl.net (8.6.9/930601.1506) id SAA19320; Thu, 8 Dec 1994 18:45:05 -0500 Received: from uucp5.UU.NET by relay1.UU.NET with SMTP id QQxtll16907; Thu, 8 Dec 1994 18:16:04 -0500 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Thu, 8 Dec 1994 18:16:20 -0500 Received: from metis.UUCP by tripos (4.1/SMI-4.0) id AA18940; Thu, 8 Dec 94 16:53:41 CST Received: by metis.UUCP (4.0/4.7) id AA25924; Thu, 8 Dec 94 16:53:21 CST From: tripos!metis!matt@uunet.uu.net (Matt Clark) Message-Id: <9412082253.AA25924@metis.UUCP> To: "Charles G. James" Cc: uunet!ccl.net!chemistry@uunet.uu.net Subject: Re: CCL:Z matrix to cartesian coord. Question In-Reply-To: Your message of Thu, 08 Dec 94 14:27:17 -0500. Date: Thu, 08 Dec 94 16:53:20 EST In general you are correct, no methods require that kind of accuracy. However I have found that having the exact same geometry for molecules is necessary for comparing results in the same program, or among different programs. I know of several cases where the truncation of decimal places in file formats can change the results of a calculation, and sometimes alter the path of a minimization when the starting structure is not close to a minimum. From helden@gaucho.ucsb.edu Thu Dec 8 21:18:21 1994 Received: from hub.ucsb.edu for helden@gaucho.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id UAA21498; Thu, 8 Dec 1994 20:38:08 -0500 Received: from gaucho.ucsb.edu by hub.ucsb.edu; id AA16443 sendmail 4.1/UCSB-2.1-sun Thu, 8 Dec 94 17:37:42 PST for chemistry@ccl.net Received: by gaucho.ucsb.edu (AIX 3.2/UCB 5.64/4.03) id AA20546; Thu, 8 Dec 1994 17:31:14 -0800 From: helden@gaucho.ucsb.edu (Gert von Helden) Message-Id: <9412090131.AA20546@gaucho.ucsb.edu> Subject: Re: CCL:Z matrix to cartesian coord. Question To: laidig@pg.com (Bill Laidig) Date: Thu, 8 Dec 1994 17:31:13 +22305458 (PST) Cc: chemistry@ccl.net In-Reply-To: <9412081715.ZM15815@morpheus.pg.com> from "Bill Laidig" at Dec 8, 94 05:15:10 pm X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 2691 > > On Dec 8, 2:27pm, Charles G. James wrote: > > Subject: CCL:Z matrix to cartesian coord. Question > > I do not mean this as an attack upon anyone or anything. However this > relates > > to information I have to pass on to undergraduates in reference to > > computational chemistry. Just this week someone on this mailing list asked > for > > a way to get 10-15 (significant?) digits, after the komma(decimal), Cartesian > > coordinates for a Ih symmetry molecule from the z matrix of a Gaussian > > 92 program. Are we at the stage where that many significant digits are given > by > > any computational chemistry method? Are we at the stage where that many > > significant digits are obtainable by any physical method used to measure > > structure? I am still warning undergraduates to beware of the number of > digits > > which can appear in calculations not connected to their measurements or their > > original input. Can I now say there are ways out there to get precision only > > formerly dreamed by spectroscopist? Are there ways to get structural > parameters > > to this precision? > > > > I believe you misunderstood the intent of the message you referred to. The > author wanted his high symmetry geometry to be converted from internal to > cartesian coordinates to 10-15 digit accuracy. The reason for this is not > that the structures are assumed to be good to this many decimal places, but > that programs that figure out symmetry from cartesian coordinates very often > need the symmetry exactly or nearly exactly before there are able to pick > it up. My interpretation is the standard 6 decimal places he has from his > g92 output file is not accurate enough for the program he is subsequently > using for it determine or to verify that the molecule really is Ih symmetry. > > Bill > It seems to me that Gaussian92 determines symmetry by symmetry opperations after which things have to be the same to within 10**-8. This default behaviour can be changed by setting iops 17 and 18 in link 2 as Iop(2/17=n,18=n) where n is the 10**-n accuracy for symmetry determination. However, I don't know how the rest of the code reacts to that. Also, in link 2 one can tell the program to punch the coordinates as I2,3E20.12 by setting iop(2/13=2). I did not try any of the above things but hope it helps. Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From lin@gkcl.ists.ca Thu Dec 8 22:18:22 1994 Received: from gkcl.ists.ca for lin@gkcl.ists.ca by www.ccl.net (8.6.9/930601.1506) id WAA22133; Thu, 8 Dec 1994 22:10:04 -0500 Received: by gkcl.ists.ca (5.61/1.34) id AA22508; Thu, 8 Dec 94 22:09:24 -0500 From: lin@gkcl.ists.ca (Delin Shen) Message-Id: <9412090309.AA22508@gkcl.ists.ca> Subject: Computation Using PC To: chemistry@ccl.net Date: Thu, 8 Dec 94 22:09:23 ADT X-Mailer: ELM [version 2.2 PL0] Dear Netters, Does anyone have experience doing comptation (ab inition and semiempirical methods) using 486 PC with UNIX operating system, which program is most suitable for this purpose? Any help will be appreciated. Lin Chemistry Department York University Toronto, Canada From toukie@zui.unizh.ch Thu Dec 8 09:57:18 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id JAA10001; Thu, 8 Dec 1994 09:57:16 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA04278; Thu, 8 Dec 94 15:57:14 +0100 X-Nupop-Charset: British Date: Thu, 8 Dec 1994 15:50:51 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <57052.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Labware drawinfg software Status: R Dear Colleagues: Does anyone know of software for use on an IBM-type PC that would enable you to draw (or insert) pictures of common organic laboratory equipment (e.g., Erlenmeyer flasks, distillation columns, &c.). I seek a sort of PC version of the old organic chemistry equipment drawing stencils that we used to have to use in introductory organic chemistry. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch