From owner-chemistry@ccl.net Fri Feb 2 03:24:29 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA11656; Fri, 2 Feb 1996 03:16:11 -0500 Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by bedrock.ccl.net (8.7.1/950822.1) id DAA04393; Fri, 2 Feb 1996 03:16:10 -0500 (EST) Received: by SECS.UCSC.EDU (MX V3.1C) id 26264; Fri, 02 Feb 1996 00:15:15 PST Date: Fri, 02 Feb 1996 00:15:10 PST From: "W. Todd Wipke" To: chemistry@ccl.net Message-ID: <0099D48B.FAA52540.26264@SECS.UCSC.EDU> Subject: Summer Undergraduate Research Fellowships (SURF) Said fellowships for 10 week summer research at UC Santa Cruz are available in Chemistry and Biochemistry. Restricted to US citizens or legal residents, must be an undergraduate (Jr or Sr) that has not graduated by June. A theme of all research programs is "molecule design", and a special seminar series for SURF students will focus on this topic during the summer. Deadline is 15 February. For details, send email to "fileserv@secs.ucsc.edu" and in the BODY of the email, put two words: SEND SURF The material will be automatically emailed to you. This program is sponsored by NSF Undergraduate Research Experience grant support. Computational Chemistry is included in this program, please inform potential candidates. -Todd Wipke Molecular Engineering Laboratory Department of Chemistry and Biochemistry University of California Santa Cruz, CA 95064 wipke@secs.ucsc.edu fax 408-459-2935 voice 408-459-2397 From vkitzing@sunny.mpimf-heidelberg.mpg.de Fri Feb 2 09:24:32 1996 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.6.10/950822.1) id JAA14555; Fri, 2 Feb 1996 09:11:25 -0500 Received: from [192.109.43.34] (mac10.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA12358; Fri, 2 Feb 96 15:10:54 +0100 Message-Id: <9602021410.AA12358@otto.mpimf-heidelberg.mpg.de> Date: Fri, 2 Feb 1996 15:10:54 +0000 To: michael mauksch From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:Mobility paradox Cc: CHEMISTRY@www.ccl.net (Computational Chemistry List) >> >> Dear colleges on the Computational Chemistry List, >> >> this morning I thought about an apparently simple problem where I do not >> know a solution jet. Consider a symmetric 1:1 electrolyte system with a >> single dielectric constant which is divided by a planar surface into a >> right hand and a left hand side. The cationic and anionic concentrations, >> cC and cA, on both sides are the same; to obtain global electro neutrality >> cC == cA is required. Exceptions from this rule are allowed only locally, >> e.g. within a few Debye length around the boundary. The ionic mobilities >> are mu1 > mu2 on the right hand side and mu2 and mu1 on the other for >> cations and anions, respectively. At equilibrium there is no problem. >> >> Now an external electric field E is applied and this creates the problem. >> On the first view one would write the individual ionic fluxes jC and jA far >> away from the central boundary: >> >> left hand side and right hand side >> >> cations jC(left) = + F mu1 E cC and jC(right) = + F mu2 E cC >> >> anions jA(left) = - F mu2 E cA and jA(right) = - F mu1 E cA >> >> where F is Faraday's constant. But this implies jC(left) != jC(right) and >> jA(left) != jA(right) which violates the particle conservation law. I would >> assume that such a problem has been discussed in literature. Has anybody >> some ideas? >> >> I will summarize the replies. >> > >I think that the current density at the cathode is > j(K)=(mu+ + mu- )F E |Z+|(n+ - (mu-/mu+)dn- - dn-(diff)) >and at the anode: > j(A)=(mu+ + mu- )F E |Z-|(n- - dn- + dn-(diff)) >and for kinetic equilibrium j(K)= j(A) obtains, because the diffusion >current dn-(diff) will balance the unequal changes in particle density >in the left and right parts of the cell which stem from the inequality >of mobility values. This may be the situation close to the boundary. But one cannot have a non-zero concentration gradient over macroscopic distances. ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) 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 joubert@ext.jussieu.fr Fri Feb 2 09:39:36 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.6.10/950822.1) id JAA14898; Fri, 2 Feb 1996 09:36:59 -0500 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id LAA29743 for ; Fri, 2 Feb 1996 11:52:11 +0100 Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Fri, 2 Feb 1996 11:52:04 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 2 Feb 1996 11:56:52 +0100 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (JOUBERT laurent) Subject: Summary "lanth. S.E. programs" A few days ago, I put this question on the CCL : >Hi all, > >Does anybody know a semi-empirical program working with lanthanides and >actinides ? >Thanks in advance for your answers. Here is the summary of all the answers I receveid. I thank you all very much for your precious help. ---------------------------------------------------------------------------- Dear Laurent, If you get any information about semi-empirical codes for lanthanides or actinides please let me know. The only one I know is REX (relativistic extended Huchel) from Prof. Pyykko in Finland. Regards, John Waite ---------------------------------------------------------------------------- Hi Laurent, ZINDO developed by Mike Zerner (Florida Uni) and N. Roesch (TU Muenchen) can deal with lanthanides. If you account EHMO as "semi-empirical", Pekka Pyykko's REX is a very good one for actinides. This program is available from pyykko@cc.helsinki.fi or from the disk in the book "Methods in Computational Chemistry", vol2, ed by Stephen Wilson. Jian ------------------------------------------------------------------------ Hi Joubert, When you say: > >Does anybody know a semi-empirical program working with lanthanides and >actinides ? > if you need a rough idea of the orbitals, charges, or dipole moment you could try Extended Huckel. The Extended Huckel module of the CAChe Worksystem by Oxford Molecular has parameters for all the elements. Extended Huckel is not suitable for geometry optimization, or accurate energies, however. I would be very interested, if you hear about a semiempirical program that gives decent geometries and energies for the third row transition metals and/or the actinides and lanthanides. The only way to model these systems electronically that I am aware of are with Effective Core Potentials using ab initio programs. Good luck. The email address I found in the CC List Archives for Michael Zerner (at Florida) is: zerner@uffsc EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (708) 637-1559 (Voice & Fax) echamot@xnet.com ------------------------------------------------------------------------- (sorry, an answer in french. If anybody is interested, I will translate it.) Cher M. JOUBERT, Merci de votre lettre d'hier. Le programme REX est en distribution libre. Si vous preferez la version PC (MS-DOS), vous trouverez une diskette dans le livre Methods in Computational Chemistry, Vol. 2, ed. S. Wilson, Wiley 1988. (Aussi bien la version Fortran que les modules executables se trouvent la`.) Si c'est plutot la version mainframe, qu'il vous faut, je vous l'enverrais volontiers. Je vous signale que c'est une methode bete et mechante, parmi les approches les plus simples a la chimie quantique. D'autre part elle est transparante et facile a interpreter. A part de OP.CIT., est-ce que vous connaissez les parametres pouri les actinides dans Pyykko-Laakkonen-Tatsumi, Inorg. Chem. 28 (1989) 1801? Pour Th - Np ce sont ces-la que je recommende. Personellement je fait la plupart des travauz actuels au niveau ab initio par des pseudopotentiels relativistes. Quand aux pseudopotentiels, nous utilisons ceux des autres, voir Pyykko-Li-Runeberg, J.Phys.Chem. 98 (1994) 4809, pour l'uranium. Meme si REX (comme toutes les methodes EHT) est plutot mauvais pour les distances de liaison, vous pourrez peut-etre limiter l'espace des conformations. La question qui se pose est, s'il n'y a pas des programmes de meca moleculaire pour cela. Bien amicalement, Pekka PYYKKO I--------------------------------------------------------I I NEW COORDINATES: I I I I Postal address: Prof. Pekka Pyykko" I I Department of Chemistry I I P.O.B. 55 (A.I. Virtasen aukio 1) I I FIN-00014 University of Helsinki I I Finland I I I I Telephone: 358-0-191 40171 I I Secretary: 358-0-191 40170 I I FAX: 358-0-191 40169 I I E-mail: Pekka.Pyykko@helsinki.fi I I--------------------------------------------------------I I Did you visit www.csc.fi/lul/rtam/ ? I ---------------------------------------------------------- -------------------------------------------------------------------------- Zerner's address is zerner@qtp.ufl.edu. As for modifications to ZINDO, Zerner sold ZINDO II to Biosym, not to CAChe (who made his program known to the world), and so we do not have the parameterizations that have been added. I do not know if the (commercial) ZINDO II has lanthanides in it or not. Certainly, they are not available in the CAChe version. -Sam -------------------------------------------------------------------------- Laurent, Try zerner@qtp.ufl.edu for Mike Zerner and pyykko@cc.helsinki.fi for Pekka Pyykko. Good luck! -------------------------------------------------------------------------- Dear Joubert, Please, take a look at our paper entitled "Sparkle model for the calculation of lanthanide complexes" which uses AM1 and appeared in Chem. Phys. Lett., 1994, 227, 349. Another paper which will be soon appearing in J.C.S., Faraday Transactions shows how to calculate the ligand electronic spectra of lanthanide complexes. If you have any doubts on how to implement our sparkle model, please feel free to contact me. Sincerely yours, ************************************************************************ * * * Alfredo Mayall Simas e-mail: AMS@npd.ufpe.br * * Departamento de Quimica Fundamental Fax: (081) 271-8442 * * Universidade Federal de Pernambuco Office: (081) 271-8440 x 37 * * 50.739-000 Recife, PE CCEN: (081) 271-8400 * * Brasil * * * ************************************************************************ ----------------------------------------------------------------------- ------------------------------------------------------------------ Laurent JOUBERT Ecole Nationale Superieure de Chimie de Paris Laboratoire d'electrochimie et de chimie analytique 11, rue Pierre et Marie Curie 75005 PARIS - FRANCE Tel : 44-27-66-94 Fax : 44-27-67-50 E-Mail : joubert@ext.jussieu.fr Website : http://www.enscp.jussieu.fr ------------------------------------------------------------------ From adrian@phy52.nist.gov Fri Feb 2 09:54:34 1996 Received: from phy52.nist.gov for adrian@phy52.nist.gov by www.ccl.net (8.6.10/950822.1) id JAA15188; Fri, 2 Feb 1996 09:52:01 -0500 Received: by phy52.nist.gov (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id JAA23942; Fri, 2 Feb 1996 09:51:24 -0800 From: "Adrian Roitberg" Message-Id: <9602020951.ZM23940@phy52.nist.gov> Date: Fri, 2 Feb 1996 09:51:20 -0800 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: copper parameters Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I am trying to work on the refinement/vibrational spectral prediciton of a copper based protein, Azurin. Said protein can exists in both reduced and oxidized states, and then the modelling can became difficult. I will try several approaches, but have founf that there seems to be a lack of proper parameters to start with. This is where my questions come: 1. Are there parameters for copper in Mopac ? Walter Thiel has a paper out with parameters for second row elements, and for the Zinc Group (JPC, 100:616-626 (1996)), but that is as close as I got. 2. Are there MM parameters for copper in either Amber or Discover ? I thank you all for your help. regards -- Adrian E. Roitberg ======================================================================== National Institute for Standards | Phone: (301) 975-4469 and Technology | Fax : (301) 330-3447 Biotechnology Division | E-mail : adrian@nist.gov Building 222, A-353 | URL : http://www.chem.nwu.edu/~adrian Gaithersburg, MD 20899 | ======================================================================== From patnaiss@Picard.ml.wpafb.af.mil Fri Feb 2 14:54:37 1996 Received: from riker.ml.wpafb.af.mil for patnaiss@Picard.ml.wpafb.af.mil by www.ccl.net (8.6.10/950822.1) id OAA20019; Fri, 2 Feb 1996 14:51:42 -0500 Received: from picard.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA24352; Fri, 2 Feb 1996 14:43:34 -0500 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA14598; Fri, 2 Feb 96 14:43:32 EST Date: Fri, 2 Feb 96 14:43:32 EST From: patnaiss@Picard.ml.wpafb.af.mil (Soumya S. Patnaik MLPJ UTC) Message-Id: <9602021943.AA14598@Picard.ml.wpafb.af.mil> To: chemistry@www.ccl.net Subject: summary on rigid body minimization Thanks to everyone who responded to my follwing query: > > Dear Colleagues, > > I am looking for a program that would do > minimization of the energy of association of two or > more molecules while considering each molecule rigid. > > Does anyone have access to such a program? Thanks in advance I got a lot of helpful information (compiled at the end of this message) and have finally decided to looking at Alex Brunger's X-plor (thanks to Tom Simonson for pointing it out to me). I think it is the most suitable for what I want to do. I am interested in modeling liquid crystals for which I would like to add an additional term to the MM potential energy function, representing the mean liquid crystalline environment. In order to see the effect of this additional term, I have to hold the molecules rigid and let them minimize the intermolecular energies by rotation and translation. I was initially planning to use the internal coordinate constrains in CHARMm to make the molecules rigid. Unfortunately, charmm does the energy minimization in cartesian coordinate space and not in internal coordinate space. Therefore using the IC constraints allows for only very small movements so ineffect the molecules get pinned to a particular cartesian space and not much rotation or translation can occur. Therefore, I was really encouraged to find out that Xplor does minimization/ dynamics in rigid body coordinate space. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Dr Soumya S. Patnaik email: patnaiss@picard.ml.wpafb.af.mil + + Materials Laboratory, Wright Patterson AFB + + usmail: WL/MLPJ, Bldg 651, 3005 P St, Ste 1, WPAFB, OH 45433-7702 + + Telephone: (513) 255-6671 ext.3116 FAX: (513) 255-1128 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -------------------------------------------------------------- We have a code that can do rigid minimizations. The minimization routines sit inside our in-hous MD code CCEMD which uses the CHARMM force field. Most of teh MD code is in C, but the constrained grad. min. routines are in Fortran. If this looks like something useful, we can let you have the source code. I am putting a copy of our initial report on the method in the mail for you. The paper mainly discusses the case of letting dihedrals move, but one of the examples has a rigid drug molecule whose position is minimized in a rigid protein binding site, which sounds similar to what you are looking for. Richard ----------------------------------------------- | Richard Judson | | Center for Computational Engineering, MS 9214 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | (510)294-2234 (FAX) | | email: rsjuds@ca.sandia.gov | | | ----------------------------------------------- From xiaopeng@astro.ocis.temple.edu Tue Jan 30 15:40:04 1996 Return-Path: Received: from astro.ocis.temple.edu by Picard.ml.wpafb.af.mil (4.1/version) id AA14465; Tue, 30 Jan 96 15:39:42 EST Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id PAA06938; Tue, 30 Jan 1996 15:39:13 -0500 (EST) Date: Tue, 30 Jan 1996 15:39:12 -0500 (EST) From: Peking To: "Soumya S. Patnaik MLPJ UTC" Cc: chemistry@www.ccl.net Subject: Re: CCL:looking for a rigid body minimization prog In-Reply-To: <9601301625.AA10051@Picard.ml.wpafb.af.mil> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: OR I think that you can construct a z-matrix format of 2 molecule separately and then put them together, specify al the parameters in the molecule as constraints. so this just leaves 3 other parameters between 2 molecule not constraint(they are distance, angle, and diherdral angle betwwen the first atom of the 2nd molecule and another atom you choose from the 1st molecule) . Then you just submit the job in G94 This does work, but a little lousy to specify the constraints xiaopeng ----------------------------------------------------------------- Chemistry Graduate Student 215-5357188(home) 215-2047149(office) xiaopeng@astro.ocis.temple.edu ----------------------------------------------------------------- From rita@biosoft.com Tue Jan 30 16:53:48 1996 Return-Path: Received: from biosoft.com by Picard.ml.wpafb.af.mil (4.1/version) id AA15544; Tue, 30 Jan 96 16:53:40 EST Received: by biosoft.com (950911.SGI.8.6.12.PATCH825/940406.SGI) for patnaiss@picard.ml.wpafb.af.mil id QAA21005; Tue, 30 Jan 1996 16:53:12 -0800 Date: Tue, 30 Jan 1996 16:53:12 -0800 From: rita@biosoft.com (Margarita Abagyan) Message-Id: <199601310053.QAA21005@biosoft.com> Apparently-To: patnaiss@picard.ml.wpafb.af.mil Status: OR Dear Soumya, ICM is a unique program which not only allows you to perform efficient local can global energy optimization with any number of rigid blocks in your molecule(s), but also has an elaborate energy function including vacuum energy, free energy of solvation if your molecule is in aqueous solution and surface energy and several types of restraints. To perform local energy minimization of two ridig molecules you invoke the following commands: build "myMolecules" display # the program has excellent graphics and you can see minimization on the screen fix v_//* # fix all the variables unfix v_2//?vt* # unfix positional variables of the second molecule minimize for global energy optimization and docking one molecule to the other you say montecarlo You can just as easily unfix any subset of potentially important variables, say, on the molecular surface. With ICM you can also manually dock two rigid molecules on the screen. You can obtain some information about us and the ICM program at http://biosoft.com If you would like to get a complete version with the program manual for trial let me know. If you have an SGI workstation, I would need the output of the sysinfo -s command With best regards, Rita, Biosoft From wally@CompChem.com Tue Jan 30 18:08:54 1996 Return-Path: Received: from ng.netgate.net by Picard.ml.wpafb.af.mil (4.1/version) id AA15977; Tue, 30 Jan 96 18:08:52 EST Received: from p90 (d27.netgate.net [205.214.160.59]) by ng.netgate.net (8.6.12/8.6.9) with SMTP id PAA07100 for ; Tue, 30 Jan 1996 15:14:27 -0800 Message-Id: <2.2.32.19960130230909.0030e3c4@ng.netgate.net> X-Sender: wally@ng.netgate.net X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 30 Jan 1996 15:09:09 -0800 To: patnaiss@Picard.ml.wpafb.af.mil (Soumya S. Patnaik MLPJ UTC) From: "Walter E. Reiher III" Subject: Re: CCL:looking for a rigid body minimization program Status: OR I wrote such a program for my thesis work a long time (10-13 years) ago and recently tried to dust it off and get it working again. It appears that I'm going to have to do it over again, as it even predates ANSI C. The last working version was under VAX/VMS and I still have an .EXE that runs on an old-fashioned VAX (not Alpha/OpenVMS). It takes a Gaussian-like Z-matrix as input and optimizes in internal coordinate space (with analytic derivatives and flexible force fields). I would be very interested in receiving a summary of the responses you receive, in the hope that I'm not going to have to re-invent it all over again. Good luck, Wally ======================================================================== Walter E. Reiher III, Ph.D. Wally@CompChem.com CompChem Innovations Consulting in computational chemsitry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 From simonson@zinfandel.u-strasbg.fr Wed Jan 31 03:05:45 1996 Return-Path: Received: from isis.u-strasbg.fr by Picard.ml.wpafb.af.mil (4.1/version) id AA17356; Wed, 31 Jan 96 03:05:43 EST Received: from zinfandel.u-strasbg.fr (zinfandel.u-strasbg.fr [130.79.79.230]) by isis.u-strasbg.fr (8.6.11/8.6.9) with SMTP id IAA10346 for ; Wed, 31 Jan 1996 08:57:28 +0100 Received: by zinfandel.u-strasbg.fr (NeXT-1.0 (From Sendmail 5.52)/NeXT-2.0) id AA08476; Wed, 31 Jan 96 09:01:36 GMT+0100 Date: Wed, 31 Jan 96 09:01:36 GMT+0100 From: simonson@zinfandel.u-strasbg.fr (Thomas Simonson) Message-Id: <9601310801.AA08476@ zinfandel.u-strasbg.fr > To: patnaiss@picard.ml.wpafb.af.mil Subject: Re: CCL:looking for a rigid body minimization prog Status: OR Dear Soumya, X-PLOR has the capability to do minimization on several rigid bodies. There's a web page at http://xplor.csb.yale.edu. Tom Simonson From chpajt@bath.ac.uk Tue Jan 30 14:24:50 1996 Return-Path: Received: from goggins.bath.ac.uk by Picard.ml.wpafb.af.mil (4.1/version) id AA13137; Tue, 30 Jan 96 14:24:45 EST Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 30 Jan 1996 18:11:14 +0000 Date: Tue, 30 Jan 1996 18:11:12 +0000 (GMT) From: A J Turner To: "Soumya S. Patnaik MLPJ UTC" Subject: Re: CCL:looking for a rigid body minimization prog In-Reply-To: <9601301625.AA10051@Picard.ml.wpafb.af.mil> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: OR Hi! This is just about achievable using charmm and the internal coordinate contrains - and or shake. Also I believe that the redundant optimiser in G94 will do it. It is possible to set up a zmatrix to do this as well - but it would be quite importants to set the matrix up correctly - or the hessian update might die. If you let me have any more info on what you want to do I might be able to help soem more. Hope this is of some use Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From chpajt@bath.ac.uk Wed Jan 31 14:23:19 1996 Return-Path: Received: from goggins.bath.ac.uk by Picard.ml.wpafb.af.mil (4.1/version) id AA22769; Wed, 31 Jan 96 14:23:16 EST Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Wed, 31 Jan 1996 16:26:13 +0000 Date: Wed, 31 Jan 1996 16:26:08 +0000 (GMT) From: A J Turner To: "Soumya S. Patnaik MLPJ UTC" Subject: Re: rigid body minimization In-Reply-To: <9601311528.AA20251@Picard.ml.wpafb.af.mil> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: OR Hi! I think I might have the answer - but it'll mean you breaking out a sweat. First put in extra bonds within your bodies. Bond everything to everything else. If you have problems joining residues this way - they will each have to be joind to the next using three non parrallel bonds. Now use the Powell, SD or CONG (I strong recommend POWELL) to minimse having put a SAKE BONDS in there. Now - if your system does still not move enough - I guess you're going to have to bite the bullet and do a quenched dynamics run - probably preceeded by a heating and equilibration. Tell me if any of this sound reasonable!! Good luck Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From heather@xhost2.tripos.com Fri Feb 2 15:24:38 1996 Received: from gatekeeper.tripos.com for heather@xhost2.tripos.com by www.ccl.net (8.6.10/950822.1) id PAA20189; Fri, 2 Feb 1996 15:10:10 -0500 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id OAA01232 for ; Fri, 2 Feb 1996 14:09:55 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma001230; Fri Feb 2 14:09:36 1996 Received: from xhost2.tripos (xhost2.tripos.com [192.160.145.213]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id OAA09864 for ; Fri, 2 Feb 1996 14:09:20 -0600 Received: by xhost2.tripos (940816.SGI.8.6.9/5.6) id UAA15519; Fri, 2 Feb 1996 20:09:28 GMT Date: Fri, 2 Feb 1996 20:09:28 GMT From: heather@xhost2.tripos.com (Heather Hunter) Message-Id: <199602022009.UAA15519@xhost2.tripos> To: chemistry@www.ccl.net Subject: Alchemy 2000 Later this Spring Tripos will release a new generation of desktop molecular modeling and analysis called Alchemy 2000. The PC version will be ready for beta testing later this month, and we still have a few openings available for dedicated beta testers. Hardware requirements include any 486 PC with 8 megabytes of RAM and at least 20 megabytes of disk space available. Features include the MM3 force field, batchmode analysis, spreadsheet and graphing capabilities, new graphics, protein builder with ribbon displays, Concord for 2D to 3D conversions, customizable tools, and more. Later in the year we will be introducing the Mac version of Alchemy 2000. Therefore, if you are a Mac user and would like to be on the beta consideration list, please contact me. For more information on the Alchemy 2000 beta program, please contact me by e-mail, phone, or fax. Thank you Heather Hunter Tripos Inc., 1699 South Hanley Rd, St. Louis MO. 63144 Phone (314) 647-1099 or 1-800-323-2960 Fax (314) 647-9241 Email heather@tripos.com From johnk@spasm.niddk.nih.gov Fri Feb 2 16:54:39 1996 Received: from alw.nih.gov for johnk@spasm.niddk.nih.gov by www.ccl.net (8.6.10/950822.1) id QAA21977; Fri, 2 Feb 1996 16:46:56 -0500 Received: from spasm.niddk.nih.gov by alw.nih.gov (5.61/1.35(alw-2.4)) id AA18922; Fri, 2 Feb 96 16:46:46 -0500 Received: by spasm.niddk.nih.gov (4.1/non-alw-1.0) id AA00709; Fri, 2 Feb 96 16:43:06 EST Date: Fri, 2 Feb 96 16:43:06 EST From: John Kuszewski Message-Id: <9602022143.AA00709@spasm.niddk.nih.gov> To: CHEMISTRY@www.ccl.net Subject: MC moveset rules Hi, I'd like to do some monte carlo simulations of proteins. All the P-chem books I've found say that you have a lot of latitude in choosing movesets for MC simulations. But there have to be *some* rules. A moveset that caused the structure to jump between only two different conformations wouldn't give you a realistic distribution, for example. Does anyone know what the rules are? Can anyone suggest a good reference that describes them? --JK