From vkitzing@sunny.mpimf-heidelberg.mpg.de Wed Nov 22 02:51:41 1995 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.6.10/950822.1) id CAA09586; Wed, 22 Nov 1995 02:38:50 -0500 Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA08136; Wed, 22 Nov 95 08:38:26 +0100 Received: by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA00888; Wed, 22 Nov 95 08:38:37 +0100 From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Message-Id: <9511220738.AA00888@sunny.mpimf-Heidelberg.mpg.de> Subject: Re: CCL:Molecular Mechanics To: 94970459@vax1.dcu.ie (Paddy Kane) Date: Wed, 22 Nov 1995 08:38:37 +0100 (MET) Cc: chemistry@www.ccl.net In-Reply-To: <01HXVTUEQ4OI96VK5U@vax1.dcu.ie> from "Paddy Kane" at Nov 20, 95 11:23:07 pm X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 1956 Dear Paddy Kane, > The reason that I ask is that I obtained the following energies from > MM optimizations for complexes of the same ligand but with different > ions: > Energy/ (kcal / mol) > Li+ -190.6 > Na+ -171.2 > K+ -150.8 > > We have found experimentally that the ligand is selective for > sodium over magnesium; so I would have expected to have obtained a > lower energy for the sodium complex. So *IF* MM optimization > energies are not a reliable indicator of selectively what exactly is > the significance of the above difference of 63 kcal / mol? I think this energy has some relevance. But in comparing the results you have to consider that in experiment you take the ions out of water and not out of vacuum. You have to include hydration energies. You have to look first which energies may be important in your experimental binding studies and than have to think about how to estimate them using MM etc. There are several levels you could use. The simplest one would be to use experimental hydration energies. The next level would be to estimate the hydration energy using the same force field. Possibly, the ligand also requires some hydration because a water molecule may be replaced by the ion. The most sophisticated, but not necessarily the most reliable, method would be to put the ligand in water and evaluate the free energy difference by mutating the water molecule closest to the binding site into an ion. This method requires very careful evaluations and will certainly take much time. ------------------------------------------------------------------------- Eberhard von Kitzing Abteilung Zellphysiologie Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.mpimf-heidelberg.mpg.de http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From owner-chemistry@ccl.net Wed Nov 22 05:21:43 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA11504; Wed, 22 Nov 1995 05:08:17 -0500 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by bedrock.ccl.net (8.7.1/950822.1) id FAA17591; Wed, 22 Nov 1995 05:06:03 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA03893 (5.65c/IDA-1.4.4); Fri, 17 Nov 1995 13:53:47 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA27366; Fri, 17 Nov 95 13:50:30 +0100 Date: Fri, 17 Nov 95 13:50:30 +0100 From: Herbert Homeier t4720 Message-Id: <9511171250.AA27366@rchs1.chemie.uni-regensburg.de> To: yu@infiniti.wavefun.com Subject: Re: G:How to keep a particular state Cc: CHEMISTRY@ccl.net, fournier@hal.Physics.Unlv.Edu, HRUSAK@jh-inst.cas.cz yu (yu@infiniti.wavefun.com) wrote: > On Nov 16, 10:44am, Herbert Homeier t4720 wrote: > > Subject: CCL:G:[Q]: How to keep a particular state in G94? .... > > > > I had a question that I hope someone on the list can help. I am > > > > doing some calculations on small transition metal compound using Gaussian > > > > 94. I carried out an SCF calculation which gives me a particular state > but > > > > I would like to calculate a DIFFERENT state. After using > > > > guess=(read,alter) to get to the state I like, the SCF brings it back to > > > > the original state that I do not want. > > > > > > > > My question is: is there anyway I can get Gaussian to keep the same > > > > state from my guess=(read,alter) job? > > > > > > > > yours sincerely, > > > > Ida N. L. Ma > > > > > > ... ..... > > excited states of the same symmetry as the ground state are saddle > > points of the functional that is minimized in a variational calculation > > (as are the excited states of the other symmetries). That would imply > > that an SCF calculation can converge to a particular excited state of > > ground state symmetry if the initial guess is close enough. (in > > principle, not paying attention to rounding errors etc.) > > > > I faintly remember that some people did a similar thing in DFT to > > obtain excited states from one-determinant wave functions. > > > > If this saddlepoint approach is in principle ok, the main problem would > > be to get accurate initial guesses. In a situation where many excited > > states are close together in energy or closely coupled (like in many > > transition metal compounds), this is expected to be rather difficult. > > > > By the way: The above should not be interpreted in the sense that I > > recommend not to use MCSCF / CI. 8^) > > ..... > > I may little insist my understanding to the priciple of quantum chemistry. In a > thermo- chemical reaction (Almost all QC studies for reactive mechanism are for > thermo- reaction.), the STATE will be kept. If you optimize the geometry, you > can get minimum (Reactant, Produncts and Intermediate (if exists)) and Saddle > point(s). All of these points are in same STATE, the ground state. Practically, > if two geometries are apart away (For example, one is close to reactant, > another is the initial guess to transition state.), it isn't easy to know if > they are in same state. IRC method may help this. If IRC can connect them, they > are in same state, otherwise they are not. > > If there exist some programs which are smart enough to get "a particular > excited state of groud state symmetry", I bet they have to make some specific > treatments to Variational Priciple. > > Best wishes! > > Jianguo Yu > > -- Hi, maybe there is some confusion about the use of the term "saddlepoint" here. There are two related but different meanings of it: A) A function(al) has a saddlepoint if all first derivatives of the function(al) vanish at that point. B) The more restricted one in quantum chemistry: A saddlepoint (in the sense A) of an energy hypersurface of a molecular system. When I was considering whether " excited states of the same symmetry as the ground state are saddle points of the functional that is minimized in a variational calculation (as are the excited states of the other symmetries)." I meant saddlepoints in the sense A, where the function under consideration is the expectation value of the energy (=the variational functional) as function of the MO coefficients. Thus, I was not talking about the energy as function of the nuclear coordinates, ie., not about a saddlepoint in the sense B. Sorry that I did not make plain enough what saddlepoint was meant. Thus, for my consideration above, one may consider a fixed geometry. Then, the problem is whether a variational calculation can converge to an excited state of the same symmetry as the ground state, even when using a single-determinant ansatz, ie., when using SCF / DFT, but not MCSCF. And, I may add, is that possible without restriction of the space of single determinant wave functions (like to those determinants that are orthogonal to the ground state). I received an Email of Rene Fournier (many thanks again!) with a list of references to excited state calculations in DFT. I include it below since it may be of more general interest, as an Email of Jan Hrusak was asking for exactly this. Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- ----- Begin Included Message ----- Subject: Excited states in DFT. Date: Thu, 16 Nov 1995 12:09:26 -0800 From: Rene Fournier Content-Length: 2972 X-Lines: 71 Status: RO Hello. Most DFT calculations of excited states take the empirical method, here are some references, about theory and about calculations: Rigorous DF theory of excitations and excited states: 1) M. E. Casida, in "Recent Advances in Density Functional Methods", Ed. D. P. Chong (World Scientific, New Jersey, 1996) (to appear soon) and references therein, including: 2) B. M. Deb and S. K. Gosh, J. Chem. Phys. 77 (1982) 342. 3) S. K. Gosh and B. M. Deb, Chem. Phys. 71 (1982) 295. 4) L. J. Bartolotti, Phys. Rev. A 24 (1981) 1661. 5) L. J. Bartolotti, Phys. Rev. A 26 (1982) 2243. 6) S. Chakravarty, M. B. Fogel, and W. Kohn, Phys. Rev. Lett. 43 (1979) 775. 7) E. Runge and E. K. U. Gross, Phys. Rev. Lett. 52 (1984) 997. 8) E. K. U. Gross and W. Kohn, Phys. Rev. Lett. 55 (1985) 2850; erratum, ibid 57 (1985) 923. 9) D. Mearns and W. Kohn, Phys. Rev A 35 (1987) 4796. 10) E. K. U. Gross and W. Kohn, Adv. Quantum Chem. 21 (1990) 255. 11) A. Zangwill and P. Soven, Phys. Rev. A 21 (1980) 1561. 12) K. Nuroh, M. J. Stott, and E. Zaremba, Phys. Rev. Lett. 49 (1982) 862. 13) A. A. Quong and A. G. Eguiluz, Phys. Rev. Lett. 70 (1993) 3955. 14) section 9.2 of R. G. Parr and W. Yang, "Density Functional Theory of Atoms and Molecules" (Oxford University Press, New York, 1989) and references therein. Slater's (semi-empirical) transition state method: 15) J. C. Slater, Adv. Quantum Chem. 6 (1972) 1. 16) A. R. Williams, R. A. deGroot, and C. B. Sommers, J. Chem. Phys. 63 (1975) 628. The "multiplet problem" in DFT, theory and calculations: 17) T. Ziegler, A. Rauk, and E. J. Baerends, Theor. Chim. Acta 43 (1977) 261. 18) U. von Barth, Phys. Rev. A 20 (1979) 1693. 19) J. S. Tse, J. Chem. Phys. 73 (1980) 5734. 20) C. Daul, H.-U. Gudel, and J. Weber, J. Chem. Phys. 99 (4023) 1993. Calculation of ionization potentials, photoelectron spectra: 21) D. P. Chong, Chem. Phys. Lett. 232 (1995) 486. 22) D. P. Chong, J. Chem. Phys. 103 (1995) 1842. 23) P. Duffy and D. P. Chong., Org. Mass Spectrometry 28 (1993) 321. 24) C. Massobrio, A. Pasquarello, and R. Car, Phys. Rev. Lett. 75 (1995) 2104. Calculation of UV-vis. excitations: 25) L. Ye, A. J. Freeman, D. E. Ellis, and B. Delley, Phys. Rev. B 40 (1989) 6277. 26) H. Ishikawa, K. Fujima, H. Adachi, E. Miyauchi, and T. Fujii, J. Chem. Phys. 94 (1991) 6740. 27) G. Gardet, F. Rogemond, and H. Chermette, Theor. Chim. Acta 91 (1995) 249. There are probably many, many early papers (1970's, 1980's) that used the Scattered-Wave (or "Multiple Scattering") X-alpha method with the Slater's transition state prescription to study the excitation spectra of mostly high-symmetry inorganic complexes (Cr(CO)_6, Ni(CO)_4, and the like) but I don't have any reference at hand. One could search by keywords or try for "J. C. Slater", "Keith H. Johnson", "David A. Case", "Louis A. Noodleman". Best regards, Rene Fournier. ----- End Included Message ----- From andreas@majestix.msp.univie.ac.at Wed Nov 22 08:06:47 1995 Received: from majestix.msp.univie.ac.at for andreas@majestix.msp.univie.ac.at by www.ccl.net (8.6.10/950822.1) id HAA13690; Wed, 22 Nov 1995 07:59:10 -0500 Received: from majestix by majestix.msp.univie.ac.at via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id NAA00812; Wed, 22 Nov 1995 13:57:39 +0100 Sender: andreas@majestix.msp.univie.ac.at Message-ID: <30B31E43.41C6@majestix.msp.univie.ac.at> Date: Wed, 22 Nov 1995 13:57:39 +0100 From: Andreas Parusel Organization: Institut f; Theoretische Chemie, Universitaet Wien X-Mailer: Mozilla 2.0b2 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CHARMM X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Sirs! I am posting here just for an information. If anybody is working with the CHARMM programm, i'd be glad if he could contact me for some questions! Thanks a lot for everybody in advance! Andreas Parusel, Vienna -- ======================================================================= _/_/ _/_/ andreas@majestix.msp.univie.ac.at = _/ _/_/ _/ andreas@phys-chemie.uni-wuerzburg.de = _/ _/_/ _/ parusel@aries.scs.uiuc.edu = _/_/ _/_/ = = Andreas Parusel Institut fuer Theoretische Chemie = Drorygasse 15/27 Althanstr. 14 = A-1030 Wien A-1030 Wien = +43 1 7519244 Tel +43 1 31336 1572 = ======================================================================= From carmen.medina@upp.pharmacia.se Wed Nov 22 08:21:44 1995 Received: from gatekeeper.pharmacia.se for carmen.medina@upp.pharmacia.se by www.ccl.net (8.6.10/950822.1) id IAA13851; Wed, 22 Nov 1995 08:10:51 -0500 From: Received: from mailgate.pharmacia.se by gatekeeper.pharmacia.se; (5.65/1.1.8.2/16Feb95/sal) id AA15021; Wed, 22 Nov 1995 14:16:27 +0100 Received: by mailgate.pharmacia.se (5.65/DEC-Ultrix/4.3/sal-950131) id AA14158; Wed, 22 Nov 1995 14:05:59 +0100 Received: from ccMail by ccsmtp.pharmacia.se (SMTPLINK V2.10.08) id AA817045972; Wed, 22 Nov 95 14:11:24 MET Date: Wed, 22 Nov 95 14:11:24 MET Message-Id: <9510228170.AA817045972@ccsmtp.pharmacia.se> To: chemistry@www.ccl.net Return-Receipt-To: carmen.medina@upp.pharmacia.se Subject: re-formatting structure files >I'd like to know if there is a software, a free-bee, on the net that > can convert a Sybyl (*.MO2) file to a PDB file. There is a free program called Babel that converts more than 30 molecular modeling file formats into each other (including MOL2 and PDB). You can ftp-it from: joplin.biosci.arizona.edu Good luck ! Carmen Medina Pharmacia & UpJohn Uppsala, Sweden carmen.medina@upp.pharmacia.se From tamasgunda@tigris.klte.hu Wed Nov 22 08:51:46 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id IAA14106; Wed, 22 Nov 1995 08:35:57 -0500 Message-Id: <199511221335.IAA14106@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Wed, 22 Nov 1995 14:22:55 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Wed, 22 Nov 1995 14:22:52 +1 Subject: Conversion of Sybyl file format to PDB file Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) > I'd like to know if there is a software, a free-bee, on the net that can > convert a Sybyl (*.MO2) file to a PDB file. > > Any help would be highly appreciated. > > Thanks in advance > -Chaya It is not a free-bee, but Mol2Mol for Windows can convert from Sybyl mol2 format to PDB file format (among many others) Mol2Mol automatically converts many of the widely used file formats in chemistry. Mol2Mol is more than just a file conversion system. It has a number of other features. If interesting, contact: Cherwell Scientific Publ .Ltd The Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA Tel: +44 (0)1865 784800 Fax: +44 (0)1865 784801 e-mail: info@cherwell.com mol2mol@cherwell.com or w3: http://www.cherwell.com/products/mol2mol Tamas ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From craig@hobbes.gh.wits.ac.za Wed Nov 22 09:21:45 1995 Received: from zaphod.gh.wits.ac.za for craig@hobbes.gh.wits.ac.za by www.ccl.net (8.6.10/950822.1) id JAA14680; Wed, 22 Nov 1995 09:09:13 -0500 Received: (from craig@localhost) by zaphod.gh.wits.ac.za (8.6.11/8.6.11) id PAA15387; Wed, 22 Nov 1995 15:59:37 +0200 Date: Wed, 22 Nov 1995 15:59:37 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@zaphod.gh.wits.ac.za To: Qu Chunxu cc: chemistry@www.ccl.net Subject: Re: CCL:cavity volume calculation In-Reply-To: <9511210136.AA25319@titbio-gw.bio.titech.ac.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Qu, > I am studying on the thermostability of 3-isopropylmalate dehydrogenase. > Protein engineering showed that at a certain site, Ala-->Leu mutation > increased the stability of protein. Crystallography analysis showed that the > sidechain of Leucine reduced the cavity around mutation site. Although the > dot surface illustration can show this point very well, we are asked to give > the cavity volume in each case. However, we have no such a program. Could you > help me? Thanks in advance. I have a program to calculate various steric effects in molecules and crystals, and recently added a cavity volume calculation to it for the calculation of the cavity volume in the region of perchlorate groups in crystals. The main way of calculating the cavity volume is using a Monte Carlo sampling approach, which gives very fast results, with moderate accuracy. There are four different cavity volumes calculated, depending on exactly what is meant by cavity volume (depends mainly on how you define the boundry to the cavity). Unfortunately the program does not yet include a cavity search algorithm, so you have to tell it exactly where the cavity is. If you're interested, the program is available at: ftp://hobbes.gh.wits.ac.za/pub/steric/steric_1.08.tgz There is a readme file for installation info, and online help, but I'd recommend you e-mail me for specific info, particularly about the cavity volume calculation, because it's quite a new addition to the program. The program was developed under linux unix, but has been compiled on several other unix's with small changes to the Makefile. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From owner-chemistry@ccl.net Wed Nov 22 13:36:49 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA19927; Wed, 22 Nov 1995 13:26:13 -0500 Received: from quartz.ciw.edu for gotthard@quartz.ciw.edu by bedrock.ccl.net (8.7.1/950822.1) id NAA21771; Wed, 22 Nov 1995 13:26:08 -0500 (EST) Received: by quartz.ciw.edu (4.1/1.6) id AA14732; Wed, 22 Nov 95 14:25:24 EST Date: Wed, 22 Nov 1995 14:25:23 -0500 (EST) From: Gotthard Saghi-Szabo X-Sender: gotthard@quartz To: gamess-users@glue.umd.edu, chemistry@ccl.net Subject: New GAMESS Version Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The current version of GAMESS is dated 22 November 1995. A short description of the most recent versions follows. November 22, 1995: Analytic gradients for closed shell MP2 can be computed. CONOPT, a new geometry search scheme for locating saddle points is implemented. Two algorithms for tracing gradient extremals on the potential energy surface are included. July 26, 1995: The quasi-Newton SCF (SOSCF) convergence procedure is extended to include ROHF and all GVB wavefunctions. The DIIS option for GVB is also enhanced. March 10, 1995: An approximate second order SCF (SOSCF) method is used for convergence of RHF wavefunctions. Analytic hessian computation now includes IR intensities and the optional computation of the polarizability tensor. The Huckel guess for ECP basis sets is improved. February 1, 1995: The Morokuma decomposition of dimer interaction energies is implemented. The spin-orbit coupling code now forms and diagonalizes the spin-orbit Hamiltonian matrix, yielding total energy levels. There is also an option for a simplistic scan of a potential energy surface. November 17, 1994: The Dynamic Reaction Coordinate, which is a classical trajectory on the ab initio potential surface, can be computed. August 11, 1994: Time dependent Hartree-Fock option permits the analytic computation of the frequency dependent polarizability, and first and second hyperpolarizabilities, for closed shell wavefunctions. These relate to many interesting NLO properties, including the electro-optic Pockels effect. July 22, 1994: A spdfg gradient package replaces the former analytic gradient integrals, and runs 3-5 times faster than the former code. The localized charge decomposition (LCD) model permits analysis of energy contributions from each Ruedenberg type localized orbital. Several important URLs concerning GAMESS : * Gamess Users' List : * Home Page : * Distribution : * Graphics : * Barchetta : * MacMolplt : How to get a copy of GAMESS : ============================== A site license for GAMESS is available at no cost to both academic and industrial users. You will be asked to print out on paper, sign, and mail a letter acknowledging the Gordon group's copyright to GAMESS. This letter also prohibits you from making copies of GAMESS except for use at your own institution. Please note the distinction between "a site license at no cost" and terms such as "public domain" or "freeware". You can request a copy of GAMESS by sending E-mail to Mike Schmidt Additional information about the process is available below. GAMESS runs on nearly all computer systems, workstations or mainframes, scalar or parallel. We have IBM RS/6000 and DEC AXP workstations, and a 6 node IBM SP2 in Ames, and these are the only machines we can guarantee will work correctly. However, versions for many other computer systems exist, including DEC VAX/VMS, IBM mainframes (MVS or VM), Cray, Intel Paragon, Thinking Machines CM-5, and HP, Sun, or SGI workstations, although not all of these will have been tested recently. -- gotthard@quartz.ciw.edu From lj1@mrc-lmb.cam.ac.uk Wed Nov 22 14:51:49 1995 Received: from ppsw4.cam.ac.uk for lj1@mrc-lmb.cam.ac.uk by www.ccl.net (8.6.10/950822.1) id OAA21328; Wed, 22 Nov 1995 14:42:52 -0500 From: Received: from server1.mrc-lmb.cam.ac.uk by lilac.csi.cam.ac.uk with SMTP-CAM (XTPP8.1) as ppsw.cam.ac.uk; Wed, 22 Nov 1995 19:41:23 +0000 Received: from alf2.mrc-lmb.cam.ac.uk by server1.mrc-lmb.cam.ac.uk (5.65) id AA28016; Wed, 22 Nov 1995 19:42:02 GMT Received: by alf2.mrc-lmb.cam.ac.uk (5.65v3.2) id AA29854; Wed, 22 Nov 1995 19:42:02 GMT Message-Id: <9511221942.AA29854@alf2.mrc-lmb.cam.ac.uk> Subject: Reference for Dickerson's NEWHEL? To: chemistry@www.ccl.net Date: Wed, 22 Nov 1995 19:42:02 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Content-Length: 739 Hello everybody! I have recently been using an implementation of the program NEWHEL91, written by Dickerson. I would like to cite the relative paper, but couldn't find any reference... is there anyone who could point me to one please? Thank you very much in advance, Luca. -------------------------------------------------------------------------------- Luca Jovine Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 2QH ENGLAND Voice: +44.1223.402443 FAX: +44.1223.213556 E-Mail: lj1@mrc-lmb.cam.ac.uk Web: http://mac308-1.mrc-lmb.cam.ac.uk/LWHP.html -------------------------------------------------------------------------------- From leclerf@MEDCN.UMontreal.CA Wed Nov 22 16:51:51 1995 Received: from harfang.CC.UMontreal.CA for leclerf@MEDCN.UMontreal.CA by www.ccl.net (8.6.10/950822.1) id QAA22890; Wed, 22 Nov 1995 16:46:05 -0500 Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by harfang.CC.UMontreal.CA with ESMTP id QAA09401 (8.6.11/IDA-1.6 for ); Wed, 22 Nov 1995 16:44:24 -0500 Received: by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id VAA03797; Wed, 22 Nov 1995 21:46:19 GMT From: leclerf@MEDCN.UMontreal.CA (Leclerc Fabrice) Message-Id: <199511222146.VAA03797@meds1.MEDCN.UMontreal.CA> Subject: SAS of nucleic acids To: chemistry@www.ccl.net Date: Wed, 22 Nov 1995 16:46:18 -0500 (EST) Cc: leclerf@medcn MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1082 Hello, I'm looking for a program that would allow me to calculate the solvent-accessible surfaces of nucleic acids, in a similar way to what was done by Charles J. Alden & Sung-Hou Kim (J. Mol Biol., 1979, 132, 411-434). If possible, this program should also permit to measure the group type exposures. The two authors cited above wrote a program to do such calculations, but I do not know if it's available. Maybe, some other programs exist. A program based on the Shrake and Rupley algorithm would be prefered. I would greatly appreciate your help. Thanks. bye, \ /\ \/ \______________________________________ /\ A--T Fabrice Leclerc (----) Departement de Biochimie G--C Universite de Montreal \/ C.P. 6128, succ. Centre-Ville /\ Montreal, Quebec H3C 3J7 T--A Canada (----) tel. +1 (514)343-6111 poste 5354 C--G fax. +1 (514)343-2177 \/ leclerf@MEDCN.UMontreal.CA /\ _____________________________________ / \ / \/ From davis@adenosine.pharm.utah.edu Wed Nov 22 17:06:51 1995 Received: from cs.utah.edu for davis@adenosine.pharm.utah.edu by www.ccl.net (8.6.10/950822.1) id QAA23046; Wed, 22 Nov 1995 16:58:19 -0500 Received: from adenosine.pharm.utah.edu by cs.utah.edu (8.6.12/utah-2.21-cs) id OAA06278; Wed, 22 Nov 1995 14:57:52 -0700 Date: Wed, 22 Nov 1995 21:57:38 GMT From: davis@adenosine.pharm.utah.edu (Darrell R. Davis) Posted-Date: Wed, 22 Nov 1995 21:57:38 GMT Message-Id: <199511222157.VAA20170@adenosine.pharm.utah.edu> Received: by adenosine.pharm.utah.edu (940816.SGI.8.6.9/5.51) id VAA20170; Wed, 22 Nov 1995 21:57:38 GMT To: lj1@mrc-lmb.cam.ac.uk CC: chemistry@www.ccl.net In-reply-to: 's message of Wed, 22 Nov 1995 19:42:02 +0000 (GMT) <9511221942.AA29854@alf2.mrc-lmb.cam.ac.uk> Subject: CCL:Reference for Dickerson's NEWHEL? Luca: If you get a reference, could you send it to me since I have used the program for a recent manuscript. -------------------------------------------------------------- Darrell R. Davis Medicinal Chemistry University of Utah -------------------------------------------------------------- From owner-chemistry@ccl.net Wed Nov 22 17:21:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id RAA23373; Wed, 22 Nov 1995 17:16:37 -0500 Received: from bioc1.biosym.com for mjf@iris120.biosym.com by bedrock.ccl.net (8.7.1/950822.1) id RAA23925; Wed, 22 Nov 1995 17:16:34 -0500 (EST) Received: from iris120.biosym.com by bioc1.biosym.com (5.64/0.0) id AA09534; Wed, 22 Nov 95 14:15:24 -0800 Received: by iris120.biosym.com (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id OAA03436; Wed, 22 Nov 1995 14:15:58 -0800 Date: Wed, 22 Nov 1995 14:15:58 -0800 From: mjf@biosym.com (Mark J Forster ) Message-Id: <199511222215.OAA03436@iris120.biosym.com> To: chemistry@ccl.net Subject: protein cavities Dear Qu, > I am studying on the thermostability of 3-isopropylmalate dehydrogenase. > Protein engineering showed that at a certain site, Ala-->Leu mutation > increased the stability of protein. Crystallography analysis showed that the > sidechain of Leucine reduced the cavity around mutation site. Although the > dot surface illustration can show this point very well, we are asked to give > the cavity volume in each case. However, we have no such a program. Could you > help me? Thanks in advance. The Quanta/Protein Health software includes a tool for locating holes in a protein structure that are typically large enough to accomodate a water molecule. The method places the protein on a 3D grid and tags grid points as either protein or solvent depending upon their proximity to a protein atom.> Once the grid points for bulk solvent around the protein are identified by a flood fill technique then the non protein grid points that remain are possible solvent sized cavities within the protein. The minimum size of the hole detected may be set by the user. Hope this helps. Best Wishes __________________________________________________________ Mark / ___ / / /| / Mark J Forster / / | / Biosym / Molecular Simulations. /__/__|/ \__O_/ 9685 Scranton Rd, /__/ | San Diego, CA 92121, USA. / | /| Tel: (619) 458 9990 / o |<-------- / | FAX: (619) 458 0136 /__ __| e-mail: mjf@biosym.com / Follower of Manchester United FC. / FA cup winners 1990, / European cup winners cup winners 1991, League cup winners 1992, / FA Premier League champions 1993, FA charity shield winners 1993/4. / FA Premier League champions AND FA cup winners 1994. /_________________________________________________________ ******************************************************************************* * DISCLAIMER: Unless indicated otherwise, everything in this note is * * personal opinion, not an official statement of Biosym / MSI * ******************************************************************************* From elewars@alchemy.chem.utoronto.ca Wed Nov 22 17:51:52 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id RAA23798; Wed, 22 Nov 1995 17:39:44 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.1/8.7.1) id RAA24771 for chemistry@www.ccl.net; Wed, 22 Nov 1995 17:39:43 -0500 (EST) Date: Wed, 22 Nov 1995 17:39:43 -0500 (EST) From: "E. Lewars" Message-Id: <199511222239.RAA24771@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: RE QUESTION ON COMPUTING STABILITY 1995 Nov 22 Errol Lewars Chem Dept Trent U, Peterborough, Ontario, CANADA Hello, With regard to the recent question by Thorsten Koch "How do I measure the stability of organic molecules? ...I compare absolute electronic energy with... a known and more or less stable isomer." There were also queries about the relevance of frontier orbitals and calculated IR frequencies. *Stability* can refer to (1) the tendency of an isolated molecule to react, perforce by isomerizing or by dissociating, or it can refer to (2) the tendency of a molecule to react with another (possibly identical) molecule. Considering (1): The calculated freqs (i.e. the calc IR spectrum) provide information about the reactivity of the isolated molecule. If there are no imaginary ("negative") freqs, the molecule can exists *as far as that particular level of calc is concerned*, that is, it is a relative minimum on the potential energy surface; it sits in a well and jiggles its all-real vibrational modes, escaping from the well at a rate that, ignoring wierd things like tunneling, depends (at least approximately) on the height of the barrier separating it from the nearest other well (or nearest plateau, for dissociation). A low-freq vibration corresponding to bond cleavage should make one suspect that at some higher computational level this freq will become imaginary, and the bond will actually break. A low-freq "vibration" that coresponds to a torsional mode would, if it were coaxed into being imaginary at a higher level, correspond to a conformational change: the molecule might still exist, but might not, say, be flat as in the input geom, but rather puckered (e.g. flat D4h cyclobutane may prefer to be D2d). The stability of a real molecule (a relative minimum) can be quantified by calculating the rate at which it goes over the lowest barrier separating it from its isomerization or dissoaciation product(s). Of course, if it's substantially the lowest-energy species on the PES then you don't have to worry about this. Stability is most intelligible if expressed as half-life at some temperature (like room temp, where most of us live). Considering (2): Comparison of the frontier orbitals (HOMO and LUMO) with those of known, similar molecules is probably wothwhile, since reaction with electrophiles and nucleophiles will be governed (to the ubiquitious first approximation) by the energies of these orbitals. Some references to calulations on the stabilities/existence of exotic organic molecules are: Oxirene and substituted oxirenes-- Vacek,..., Schaefer,..., J Phys Chem 98 (1994) 8660. Fowler, Galbraith, Vacek and Schaefer, J Am Chem Soc 116 (1994) 9311. Scott, Nobes, Schaefer and Radom, J Am Chem Soc 116 (1994) 10159 N6 (e.g. hexaazabenzene), N8, etc-- Engelke, J Am Chem Soc 115 (1993) 2961 Engelke, J Org Chem 57 (1992) 4841 Engelke and Stine, J Phys Chem 94 (1990) 5689 ["Is N8 Cubane Stable?] Engelke, J Phys Chem 94 (1990) 6924 /|\ Engelke, J Phys Chem 96 (1992) 10789 | Engelke, J Phys Chem 93 (1989) 5722 | STABLE Benzooxirene-- Lewars, THEOCHEM 1996 CO2 polymers-- Lewars, THEOCHEM 1996 From raman@bioc01.uthscsa.edu Wed Nov 22 19:21:53 1995 Received: from ELZIP.UTHSCSA.EDU for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id TAA24864; Wed, 22 Nov 1995 19:10:20 -0500 Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V4.3-13 #8477) id <01HXYBIA1Y40007OLL@uthscsa.edu>; Wed, 22 Nov 1995 18:09:23 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA05291; Wed, 22 Nov 95 18:09:35 CST Date: Wed, 22 Nov 1995 18:09:28 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: CCL:cavity volume calculation In-reply-to: <9511210136.AA25319@titbio-gw.bio.titech.ac.jp> from "Qu Chunxu" at Nov 21, 95 10:36:23 am To: quchunxu@bio.titech.ac.jp (Qu Chunxu) Cc: chemistry@www.ccl.net Message-id: <9511230009.AA05291@bioc01.uthscsa.edu> X-Envelope-to: chemistry@www.ccl.net X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Content-length: 2338 Qu: > I am studying on the thermostability of 3-isopropylmalate dehydrogenase. > Protein engineering showed that at a certain site, Ala-->Leu mutation > increased the stability of protein. Crystallography analysis showed that the > sidechain of Leucine reduced the cavity around mutation site. Although the > dot surface illustration can show this point very well, we are asked to give > the cavity volume in each case. However, we have no such a program. Could you > help me? Thanks in advance. In my opinion, the best program to do volume calculations on Protein structures is that written by Fred Richards (Yale U.) called VOLUME. It employs the Voronoi method to accomplish the volume calculations. You can obtain the source from Patrick Fleming: fleming@cs.yale.edu. It can be compiled with ease on any Unix platform. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From raman@bioc01.uthscsa.edu Wed Nov 22 19:27:20 1995 Received: from ELZIP.UTHSCSA.EDU for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id TAA24831; Wed, 22 Nov 1995 19:07:24 -0500 Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V4.3-13 #8477) id <01HXYBEOGONK006X7X@uthscsa.edu>; Wed, 22 Nov 1995 18:06:29 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA05273; Wed, 22 Nov 95 18:06:40 CST Date: Wed, 22 Nov 1995 18:06:36 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: CCL:SAS of nucleic acids In-reply-to: <199511222146.VAA03797@meds1.MEDCN.UMontreal.CA> from "Leclerc Fabrice" at Nov 22, 95 04:46:18 pm To: leclerf@MEDCN.UMontreal.CA (Leclerc Fabrice) Cc: chemistry@www.ccl.net Message-id: <9511230006.AA05273@bioc01.uthscsa.edu> X-Envelope-to: chemistry@www.ccl.net X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Content-length: 2382 Fabrice: > I'm looking for a program that would allow me to calculate the > solvent-accessible surfaces of nucleic acids, in a similar way to what > was done by Charles J. Alden & Sung-Hou Kim (J. Mol Biol., 1979, 132, > 411-434). If possible, this program should also permit to measure the > group type exposures. The two authors cited above wrote a program to > do such calculations, but I do not know if it's available. Maybe, some > other programs exist. A program based on the Shrake and Rupley algorithm > would be prefered. One of the common algorithms for doing what you are asking has been implemented by Fred Richards (Yale) in a program called ACCESS. This is the de facto standard for calculating protein solvent accessible surface areas. You can obtain ACCESS by contacting Patrick Fleming at: fleming@cs.yale.edu. Pat has ported the VAX code to Unix. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From surat@nwg.nectec.or.th Wed Nov 22 22:36:56 1995 Received: from nwg.nectec.or.th for surat@nwg.nectec.or.th by www.ccl.net (8.6.10/950822.1) id WAA26996; Wed, 22 Nov 1995 22:29:53 -0500 Received: by nwg.nectec.or.th (8.6.8/1.34) id KAA04602; Thu, 23 Nov 1995 10:30:42 +0700 Received: from localhost.nectec.or.th by nwg.nectec.or.th (8.6.8/1.34) id KAA04602; Thu, 23 Nov 1995 10:30:42 +0700 Date: Thu, 23 Nov 1995 10:30:41 +0700 (GMT+0700) From: Surat Meekhanthong To: chemistry@www.ccl.net Subject: workshop on Radiation Chem. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Radiation Chemisty Group, Chemistry Division, Office of Atomic Energy for Peace, Bangkok, Thailand---with the assistance from IAEA. The Group is organiziong a 2-weeks workshop on the 1st National Trainig Course on Radiation Chemistry and its Application to be held in Bangkok, during 4-16 December 1995. The training will include lectures on basis principle of radiation chemistry and adjoining topics, its application in various fields, laboratory practices as well as excursiion to the related facilities. ***************************------------------------------- * Surat Meekhanthong * Phone (662) 579-5230 ext 322 * Office of * * Atomic Energy for Peace * E-mail . . . * Thailand. * surat@nwg.nectec.or.th ***************************------------------------------- From owner-chemistry@ccl.net Wed Nov 22 22:51:56 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA27227; Wed, 22 Nov 1995 22:49:43 -0500 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.7.1/950822.1) id WAA25504; Wed, 22 Nov 1995 22:49:39 -0500 (EST) Received: by rani.chem.yale.edu; Wed, 22 Nov 95 22:49:41 -0500 From: Dongchul Lim Message-Id: <9511230349.AA07325@rani.chem.yale.edu> Subject: SAS of nucleic acids To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 22 Nov 95 22:49:39 EST X-Mailer: ELM [version 2.3 PL11] Searching Web pages resulted in the following packages: Naccess v2.0 - Atomic solvent accessible areas http://www.biochem.ucl.ac.uk/~roman/naccess/naccess.html Naccess calculates the accessible area of a molecule from a PDB file. The program uses the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method, whereby a probe of given radius is rolled around the surface of the molecule, and the path traced out by its centre is the accessible surface. Typically, the probe has the same radius as water (1.4 Angstroms) and hence the surface described is often referred to as the solvent accessible surface. Ray Casting and Protein Geometry http://www.chem.duke.edu/research/prisant/protein/protein.html SURF http://www.cs.unc.edu/ftp/pub/projects/GRIP/SURF SURF is a set of programs for generating and displaying the solvent accessible surface of a molecule. A representation of a typical protein molecule can be generated in about a second, allowing near real-time response to changes in the surface parameters. RASMOL http://www.bio.cam.ac.uk/doc/rasmol.html The RasMol set solvent command is used to control the behaviour of the RasMol dots command. Depending upon the value of the solvent parameter, the dots command either generates a Van der Waal's or a solvent acessible surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol radius parameter. The command set solvent false, the default value, indicates that a Van der Waal's surface should be generated and resets the value of radius to zero. The command set solvent true indicates that a `Connolly' or `Richards' solvent accessible surface should be drawn and sets the radius parameter, the solvent radius, to 1.2 Angstroms (or 300 RasMol units). --------------------------------------------------------------------------- Dongchul Lim Department of Chemistry Yale University