From chemistry-request@server.ccl.net Fri Jun 21 08:30:10 2002 Received: from rasmus.uib.no (exim@[129.177.12.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LCUAa29008 for ; Fri, 21 Jun 2002 08:30:10 -0400 Received: from pc-212-202.pki.uib.no (teigen212202) [129.177.212.202] by rasmus.uib.no for chemistry@ccl.net with esmtp (Exim 3.35) id 17LNXn-00065h-00; Fri, 21 Jun 2002 14:29:39 +0200 Message-Id: <4.2.2.20020621141334.00a1c640@rasmus.uib.no> X-Sender: mbike@rasmus.uib.no X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Fri, 21 Jun 2002 14:28:18 +0200 To: chemistry@ccl.net From: Knut Teigen Subject: isoelectric point calculation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-checked-clean: by exiscan on rasmus X-Scanner: 92f373b7ceb154ac9cd8df6a15e8a521 http://tjinfo.uib.no/virus.html X-UiB-SpamFlag: NO UIB: -7 hits, 8 required; Dear CCL'ers Could somebody please tell me if there is a code or software available that can calculate the isoelectric point of a folded protein? I would like to calculate the isoelectric point based on the 3D structure, and not based purely on the primary sequence. Kind regards Knut Teigen Ph.D. student Faculty of Medicine Dept. of Biochemistry University of Bergen, Norway knut.teigen@pki.uib.no From chemistry-request@server.ccl.net Fri Jun 21 08:53:05 2002 Received: from cirse.saclay.cea.fr ([132.166.192.127]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LCr5a29411 for ; Fri, 21 Jun 2002 08:53:05 -0400 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Internet.1.0) with ESMTP id g5LCr4Zj008470 for ; Fri, 21 Jun 2002 14:53:04 +0200 (MEST) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.2.10) with ESMTP id for ; Fri, 21 Jun 2002 14:48:29 +0200 Received: from petunia.bruyeres.cea.fr (petunia.bruyeres.cea.fr [132.165.64.1]) by muguet.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Interne.1.0) with ESMTP id g5LCr4C7029263 for ; Fri, 21 Jun 2002 14:53:04 +0200 (MEST) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by petunia.bruyeres.cea.fr (8.9.3+Sun/jtpda-5.3.2) with ESMTP id OAA12368 for ; Fri, 21 Jun 2002 14:52:51 +0200 (MET DST) Received: by styx.bruyeres.cea.fr; id OAA09147; Fri, 21 Jun 2002 14:53:03 +0200 (MET DST) Message-Id: <200206211253.OAA09147@styx.bruyeres.cea.fr> Sender: beaucams@ripault.cea.fr Date: Fri, 21 Jun 2002 14:48:05 +0200 From: Sylvain BEAUCAMP X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: help about TINKER for optimize rigid molecules in cristal cell Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi there. I was wondering if anyone know if I can use TINKER for minimize coordinates and cell parameters of cristal structure with rigid molecules in the unit cell. Actually, I use Tinker with optrigid but I can optimize the cell parmeters. Many thanks for your help Sincerely Sylvain From chemistry-request@server.ccl.net Fri Jun 21 09:54:35 2002 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LDsYa30591 for ; Fri, 21 Jun 2002 09:54:35 -0400 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with ESMTP id KAA31782 for ; Fri, 21 Jun 2002 10:54:25 -0300 Date: Fri, 21 Jun 2002 10:54:25 -0300 (BSC) From: antonio luiz oliveira de noronha X-X-Sender: noronha@dedalus To: chemistry@ccl.net Subject: GAMESS on a 900MHz Athlon Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HI I'm having a weird problem with my Athlon. It was running fine doing DFT calculations for organometallic compounds for the last 3 months. In the last 3 weeks it crashes constantly, actually, every day. I though that could be a hacker, and dinsconnect the network cable, butthe problem remains. I also checked for the size of the files, and they don look to be bigger than 2GB ( I'm doing direct calculations ). Any one has ever had this problem?? Or has a tip for the solution?? I will appreciate any help Thank you ______________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |EEPEMM - Eletronic Spectra and Electromagnetic Properties of Molecules| |Theoretical Physical Chemistry | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5757 - FAX +55 31 499 5700 | |______________________________________________________________________| From chemistry-request@server.ccl.net Fri Jun 21 03:47:07 2002 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5L7l7a24352 for ; Fri, 21 Jun 2002 03:47:07 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id DAA03192 for ; Fri, 21 Jun 2002 03:47:07 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id g5L7l1U05723 for chemistry@ccl.net; Fri, 21 Jun 2002 03:47:01 -0400 (EDT) From: Wai-To Chan Message-Id: <200206210747.g5L7l1U05723@curl.gkcl.yorku.ca> Subject: wavefunction stability issues To: chemistry@ccl.net Date: Fri, 21 Jun 2002 03:46:59 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit >Date: Wed, 29 May 2002 18:29:02 +0200 >From: Patrick Bultinck >Dear all, >Can anybody refer me to a good reference on the different sources of wave >function instability ? Especially as on how to judge whether a certain post >SCF calculation will help. Also, it is sometimes stated that wave function >instability would indicate the necessity of electron correlation. At this >day and age, only single reference (Hartree-Fock) dynamical electron >correlation techniques can be used for the larger molecules I am looking >at. What good is MP2, CC etc. when the reference is not appropriate ? I don't think there is a clear-cut answer to your question. Switching to a reference UHF wavefunction in the region of a PES for a closed-shell system where the RHF wave is unstable towards spin-symmetry breaking sounds theoretically more rigourous. To my knowledge it is not known whether a UHF-based MPn or CCSD(T) method would always give more accurate result than if you stick to the unstable RHF wavefunction. At least from my limited experience if the degree of distortion of the structure calcluated and its degree of wavefunction instability are not too high it may be prudent to stick with RMP2 or RDFT for transition structure optimization to avoid spin contamination of the stable UHF wavefunction. These two references may be helpful to you: "Evaluation of S^2 for correlated wavefunctions...." Chen and Schlegel, J chem phys, vol 101 (1994) 5957. "Spin-contamination of coupled-cluster wave functions" A Krylov, J chem phys, vol 113 (2000) 6052. The Schlegel paper compares the performances of variuos R and U method with full CI on potential curve calculations. It also reports the degree of spin-contamination of the correlated wavefunctions that allows you to judge which method can best handle an unstable reference wavefunction. >Really, for a good result a technique like mrci would be very interesting, >but for some systems (and computer resources), even a large CAS+PT is >impossible. So how to handle this ? Any references ? At present analytical gradient is available in neither method. It is safe to say that their applications to calculation of ground state as an alternate to single-reference method will be limited for some time. You may check out this paper for an example of possibly an unusually large-scale CASMP2 calculations on a system presumably not amenable to single-reference method. I would be delighted to see some comparisons between CASMP2 and the single-reference BD(T) method in this subject. "UDFT and MSCF description of the photochemical Bergman cyclization of enediynes" Clark, Davidson and Zaleski JACS, vol 123 (2001) 2650. >As a side question: would anybody have any idea what percentage of post-scf >calculations being done has ever had the stability of its HF reference >checked ? Perhaps the real question is how often stability of HF reference is an issue in studies involving post-scf calculations. In principle instability of RHF wavefunction could be solved by using a MCSCF approach which in practice is not straightforward to apply. My view is there is not much one can do beyond standard methods in dealing with wavefunction instability in the intermediate bond-breaking region. Instability of UHF wavefunctions of radicals towards spatial symmetry breaking is hardly an overlooked issue. You may find this example of interest "A detailed study on the symmetry breaking and its effect on the potential surface of NO3" Eisfeld and Morokuma J chem phys, vol 113 (2000) 5587. This one concerns DFT but is still relevant "On the performance of density functional theory for symmetry-breaking problems" Sherill, Lee and Head-Gordon Chem phys lett, vol 302 (1999) 425. One area where some people may overlook the stability issue concerns singlet diradicals. This paper convers two previous studies where use of unstable RDFT wavefunctions lead to erroneous observations. J phys chem A, vol 104 (2000) 1748 Grafenstein, Hjerpe, Kraka and Cremer Wai-To Chan >Thanks, >Patrick Bultinck >Ghent University >Belgium From chemistry-request@server.ccl.net Fri Jun 21 08:58:09 2002 Received: from dori.rl.ac.uk ([130.246.135.159]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LCw8a29567 for ; Fri, 21 Jun 2002 08:58:09 -0400 Received: from kohn.nd.rl.ac.uk.nd.rl.ac.uk (kohn.nd.rl.ac.uk [130.246.48.218]) by dori.rl.ac.uk (8.11.1/8.11.1) with ESMTP id g5LCw6j13286 for ; Fri, 21 Jun 2002 13:58:06 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15635.8926.310772.589229@kohn.nd.rl.ac.uk> Date: Fri, 21 Jun 2002 13:58:06 +0100 To: chemistry@ccl.net Subject: Brenner potential code X-Mailer: VM 7.07-rfhacked under 21.4 (patch 8) "Honest Recruiter" XEmacs Lucid From: "Keith Refson" I am looking for any public domain/open source code which can handle the Brenner potential. I found some reference to various code at http://www.rahul.net/pcm/brenner/ and http://www2.zyvex.com/DCAD/Software.html but neither of these sites appear to exist -- or at least be reachable > from here. Does anyone have a pointer, or a copy of the released code? Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 446652 K.Refson@ F: 01235 445720 @rl.ac.uk From chemistry-request@server.ccl.net Fri Jun 21 10:12:22 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LECMa31026 for ; Fri, 21 Jun 2002 10:12:22 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA02664; Fri, 21 Jun 2002 10:12:20 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D133444.98ED0CEC@cornell.edu> Date: Fri, 21 Jun 2002 10:12:20 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Sylvain BEAUCAMP CC: CHEMISTRY@ccl.net Subject: Re: CCL:help about TINKER for optimize rigid molecules in cristal cell References: <200206211253.OAA09147@styx.bruyeres.cea.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I don't know if TINKER is able to do this, but Xplor (CNS) can define rigid bodies and minimize in Euler coordinates and has some abilities to impose some symmetry constraints. As you know, you cannot simply apply periodic boundary conditions since that would fix the cell. You need to allow the unit cell vectors in the periodic boundaries to vary. I have seen a paper that does this for dynamics (sorry, the reference is at home ... I will try to post it later). It was suggested to me by someone earlier on this list so you can also find it by searching the archives. I don't know of any available program able to do this, but groups that simulate crystallization must deal with the issue. BTW, crystallographic water molecules and counter ions can be quite important in the case, if they are well resolved in the structures. Richard Gillilan MacCHESS Cornell From chemistry-request@server.ccl.net Fri Jun 21 11:26:22 2002 Received: from sirius.chem.vt.edu (IDENT:root@[128.173.181.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LFQMa00319 for ; Fri, 21 Jun 2002 11:26:22 -0400 Received: from localhost (crawdad@localhost) by sirius.chem.vt.edu (8.11.0/8.11.0) with ESMTP id g5LFQLo17711; Fri, 21 Jun 2002 11:26:21 -0400 X-Authentication-Warning: sirius.chem.vt.edu: crawdad owned process doing -bs Date: Fri, 21 Jun 2002 11:26:21 -0400 (EDT) From: "T. Daniel Crawford" X-Sender: To: Wai-To Chan cc: Subject: Re: CCL:wavefunction stability issues In-Reply-To: <200206210747.g5L7l1U05723@curl.gkcl.yorku.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We have done a number of studies directly addressing the question as to how post-HF methods perform when reference functions are unstable. My experience with spatial symmetry breaking is that a strong instability in the MO's (i.e., a negative eigenvalue in the MO Hessian/stability matrix) is often not a problem (apart from practical difficulties such as finite-difference vibrational analyses). The difficult cases occur when the MO Hessian is nearly singular, that is, when one of its eigenvalues is close to zero, regardless of sign. In such cases, even high-level coupled cluster cases can give anomolous results --- e.g., vibrational frequencies > 5000 cm-1. Please see: @Article{ author = "T. D. Crawford and J. F. Stanton and W. D. Allen and H. F. Schaefer", title = "Hartree-Fock orbital instability envelopes in highly correlated single-reference wavefunctions", journal = JCP, year = 1997, volume = 107, number = 24, pages = 10626 } for a detailed theoretical analysis of this. Also, for a difficult singlet diradical case: @Article{ author = "T. D. Crawford and E. Kraka and J.F. Stanton and D. Cremer," title = "Problematic p-Benzyne: Orbital Instabilities, Biradical Character, and Symmetry Breaking", journal = JCP, year = 2001, volume = 114, pages = "10638-10650" } In this above, we applied a wide range of reference functions, including Brueckner, GVB, RHF, and UHF, to the p-benzyne diradical. -Daniel -- T. Daniel Crawford Department of Chemistry crawdad@vt.edu Virginia Tech www.chem.vt.edu/chem-dept/crawford Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From chemistry-request@server.ccl.net Fri Jun 21 10:30:59 2002 Received: from pony.its.uwo.ca ([129.100.2.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LEUwa31493 for ; Fri, 21 Jun 2002 10:30:59 -0400 Received: from femail.its.uwo.ca (hurdle.its.uwo.ca [129.100.2.108]) by pony.its.uwo.ca (8.12.1/8.12.0) with ESMTP id g5LEUtiR021775 for ; Fri, 21 Jun 2002 10:30:58 -0400 (EDT) Received: from woolabpcvsj70k (woolabpc3.chem.uwo.ca [129.100.61.41]) by femail.its.uwo.ca (8.12.1/8.12.0) with SMTP id g5LEUeFq004660 for ; Fri, 21 Jun 2002 10:30:40 -0400 (EDT) Message-ID: <00fe01c21930$32a4a210$293d6481@woolabpcvsj70k> From: "sdecker" To: Subject: Graphics Programs for Visualizing ADF MOs Date: Fri, 21 Jun 2002 10:30:31 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00FB_01C2190E.AB52EBD0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00FB_01C2190E.AB52EBD0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello All, I am relatively new to the ADF DFT package and I was wondering if = someone could point me to a good molecular graphics viewer for ADF jobs. = In particular I am interested in viewing molecular structures, = Molecular Orbitals and animating vibrational frequencies with it. =20 Thanks in advance. Sincerely, Stephen A. Decker _________________________________________________ Dr. Stephen A. Decker, Ph.D. NSERC Postdoctoral Fellow Department of Chemistry =20 University of Western Ontario London, Ontario, Canada N6A 5B7 phone: (519)-661-2111 ext. 86353 =20 fax: (519)-661-3022 email: sdecker@uwo.ca _________________________________________________ ------=_NextPart_000_00FB_01C2190E.AB52EBD0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello All,
 
    I am relatively new = to the ADF=20 DFT package and I was wondering if someone could point me to a good = molecular=20 graphics viewer for ADF jobs.  In particular I am interested in = viewing=20 molecular structures, Molecular Orbitals and animating vibrational = frequencies=20 with it. 
 
    Thanks in = advance.
 
    = Sincerely,
 
    Stephen A. = Decker
 
_________________________________________________
 
 Dr. Stephen A. Decker, = Ph.D.
 NSERC=20 Postdoctoral Fellow
 
 Department of Chemistry =20
 University of Western Ontario
 London, Ontario, =20 Canada
 N6A 5B7
 
 phone: (519)-661-2111 ext.=20 86353         =20
 fax:     =20 (519)-661-3022
 email:  sdecker@uwo.ca
____________________= _____________________________
------=_NextPart_000_00FB_01C2190E.AB52EBD0-- From chemistry-request@server.ccl.net Fri Jun 21 11:19:43 2002 Received: from venus.phpwebhosting.com ([64.29.16.27]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5LFJha32610 for ; Fri, 21 Jun 2002 11:19:43 -0400 Received: (qmail 25628 invoked by uid 508); 21 Jun 2002 15:19:36 -0000 Received: from unknown (HELO hydrogen.leitl.org) (62.226.149.82) by venus.phpwebhosting.com with SMTP; 21 Jun 2002 15:19:36 -0000 Received: from localhost (eugen@localhost) by hydrogen.leitl.org (8.11.6/8.11.6) with ESMTP id g5LFJWX20945; Fri, 21 Jun 2002 17:19:33 +0200 X-Authentication-Warning: hydrogen.leitl.org: eugen owned process doing -bs Date: Fri, 21 Jun 2002 17:19:32 +0200 (CEST) From: Eugen Leitl To: Keith Refson cc: Subject: Re: CCL:Brenner potential code In-Reply-To: <15635.8926.310772.589229@kohn.nd.rl.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 21 Jun 2002, Keith Refson wrote: > I am looking for any public domain/open source code which can handle > the Brenner potential. I found some reference to various code at Try http://www.fungible.com/fungimol/ -- Eugen P.S. sorry for public answer, but your blackhole rules are overzealous: : 130.246.135.154 does not like recipient. Remote host said: 550 5.7.1 ... Mail from 64.29.16.27 refused by blackhole site formmail.relays.monkeys.com Giving up on 130.246.135.154. From chemistry-request@server.ccl.net Fri Jun 21 15:37:50 2002 Received: from bellerophon.cnchost.com ([207.155.248.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LJbna06076 for ; Fri, 21 Jun 2002 15:37:50 -0400 Received: (root@localhost) by bellerophon.cnchost.com id PAA27658; Fri, 21 Jun 2002 15:37:49 -0400 (EDT) [ConcentricHost SMTP Relay 1.14] Message-ID: <200206211937.PAA27658@bellerophon.cnchost.com> Errors-To: From: Guillermo A Morales To: CHEMISTRY@ccl.net Reply-To: morales@combichemlab.com Subject: Computational solutions for the PC to prepare molecules for docking experiments. Date: Fri, 21 Jun 2002 12:37:49 -0700 (PST) In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, I am trying to prepare compounds for docking experiments and for this I use PC-available programs (Windows and Linux). When molecular structures are created or modified (i.e. ligand extracted from an pdb file) their coordinates are set relative to their own internal x,y,z points of origin. My problem is that the coordinates of the molecules need to be modified so the molecules are positioned at specific places relatively to the protein of interest for docking. Do you know how of any program for the PC (Windows or Linux) that allows the manipulation of molecular structures so they can be re-oriented and saved (with their internal cooridantes reflecting the new 3-D position and orientation) for their use in docking experiments? I'll summarize the answers I receive and post them here later. Thank you very much for your help in advance. Sincerely, Guillermo. -- Guillermo A. Morales Email: morales@combichemlab.com Website: http://www.combichemlab.com Member of Combi-Web Consortium: http://www.combi-web.com From chemistry-request@server.ccl.net Fri Jun 21 11:49:29 2002 Received: from smtp-gateway.jenapharm.de ([62.180.96.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5LFnSa01286 for ; Fri, 21 Jun 2002 11:49:28 -0400 To: "sdecker" Cc: chemistry@ccl.net X-Mailer: Lotus Notes Version 5.0.2c (Intl) 08 Februar 2000 Message-ID: From: Alexander.Hillisch@Jenapharm.de Date: Fri, 21 Jun 2002 17:49:18 +0200 Subject: Antwort: CCL:Graphics Programs for Visualizing ADF MOs X-MIMETrack: Serialize by Router on JE0015/JE/SRV/SHG(Release 5.07a |May 14, 2001) at 21.06.2002 17:52:21 MIME-Version: 1.0 Content-type: multipart/mixed; Boundary="0__=C1256BDF00572D258f9e8a93df938690918cC1256BDF00572D25" Content-Disposition: inline --0__=C1256BDF00572D258f9e8a93df938690918cC1256BDF00572D25 Content-type: text/plain; charset=us-ascii Hi Stephen, have a look at MOLEKEL (http://www.cscs.ch/molekel/). This program is ideally suited for the type of applications you are thinking about - and it is freely available. Best regards, Alexander ------------------------------------------------------------------------------ Dr. Alexander Hillisch EnTec GmbH Structural Bioinformatics and Drug Design Adolf-Reichwein-Str. 20 Phone: +49-3641-65-8430 D-07745 Jena, Mobile: +49-170-7521496 GERMANY Fax: +49-3641-65-8436 e-Mail: alexander.hillisch@jenapharm.de URL: http://www.entec-jena.de "sdecker" Gesendet von: "Computational Chemistry List" 21.06.02 16:30 Kopie: Thema: CCL:Graphics Programs for Visualizing ADF MOs Hello All, I am relatively new to the ADF DFT package and I was wondering if someone could point me to a good molecular graphics viewer for ADF jobs. In particular I am interested in viewing molecular structures, Molecular Orbitals and animating vibrational frequencies with it. Thanks in advance. Sincerely, Stephen A. Decker _________________________________________________ Dr. Stephen A. Decker, Ph.D. NSERC Postdoctoral Fellow Department of Chemistry University of Western Ontario London, Ontario, Canada N6A 5B7 phone: (519)-661-2111 ext. 86353 fax: (519)-661-3022 email: sdecker@uwo.ca (See attached file: C.htm) --0__=C1256BDF00572D258f9e8a93df938690918cC1256BDF00572D25 Content-type: text/html; name="C.htm" Content-Disposition: attachment; filename="C.htm" Content-transfer-encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWlzby04ODU5LTEiPg0KPE1FVEEgY29udGVudD0iTVNIVE1M IDYuMDAuMjcxMy4xMTAwIiBuYW1lPUdFTkVSQVRPUj4NCjxTVFlMRT48L1NUWUxFPg0KPC9IRUFE Pg0KPEJPRFkgYmdDb2xvcj0jZmZmZmZmPg0KPERJVj48Rk9OVCBmYWNlPUFyaWFsIHNpemU9Mj5I ZWxsbyBBbGwsPC9GT05UPjwvRElWPg0KPERJVj48Rk9OVCBmYWNlPUFyaWFsIHNpemU9Mj48L0ZP TlQ+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9QXJpYWwgc2l6ZT0yPiZuYnNwOyZuYnNw OyZuYnNwOyBJIGFtIHJlbGF0aXZlbHkgbmV3IHRvIHRoZSBBREYgDQpERlQgcGFja2FnZSBhbmQg SSB3YXMgd29uZGVyaW5nIGlmIHNvbWVvbmUgY291bGQgcG9pbnQgbWUgdG8gYSBnb29kIG1vbGVj dWxhciANCmdyYXBoaWNzIHZpZXdlciBmb3IgQURGIGpvYnMuJm5ic3A7IEluIHBhcnRpY3VsYXIg SSBhbSBpbnRlcmVzdGVkIGluIHZpZXdpbmcgDQptb2xlY3VsYXIgc3RydWN0dXJlcywgTW9sZWN1 bGFyIE9yYml0YWxzIGFuZCBhbmltYXRpbmcgdmlicmF0aW9uYWwgZnJlcXVlbmNpZXMgDQp3aXRo IGl0LiZuYnNwOyA8L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9QXJpYWwgc2l6ZT0yPjwv Rk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgZmFjZT1BcmlhbCBzaXplPTI+Jm5ic3A7Jm5i c3A7Jm5ic3A7IFRoYW5rcyBpbiBhZHZhbmNlLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgZmFj ZT1BcmlhbCBzaXplPTI+PC9GT05UPiZuYnNwOzwvRElWPg0KPERJVj48Rk9OVCBmYWNlPUFyaWFs IHNpemU9Mj4mbmJzcDsmbmJzcDsmbmJzcDsgU2luY2VyZWx5LDwvRk9OVD48L0RJVj4NCjxESVY+ PEZPTlQgZmFjZT1BcmlhbCBzaXplPTI+PC9GT05UPiZuYnNwOzwvRElWPg0KPERJVj48Rk9OVCBm YWNlPUFyaWFsIHNpemU9Mj4mbmJzcDsmbmJzcDsmbmJzcDsgU3RlcGhlbiBBLiBEZWNrZXI8L0ZP TlQ+PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9QXJpYWwgc2l6ZT0yPjwvRk9OVD4mbmJzcDs8L0RJ Vj4NCjxESVY+PEZPTlQgZmFjZT1BcmlhbCANCnNpemU9Mj5fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fPC9GT05UPjwvRElWPg0KPERJVj4mbmJzcDs8L0RJ Vj4NCjxESVY+PEZPTlQgZmFjZT1BcmlhbCBzaXplPTI+Jm5ic3A7RHIuIFN0ZXBoZW4gQS4gRGVj a2VyLCBQaC5ELjxCUj4mbmJzcDtOU0VSQyANClBvc3Rkb2N0b3JhbCBGZWxsb3c8L0ZPTlQ+PC9E SVY+DQo8RElWPiZuYnNwOzwvRElWPg0KPERJVj48Rk9OVCBmYWNlPUFyaWFsIHNpemU9Mj4mbmJz cDtEZXBhcnRtZW50IG9mIENoZW1pc3RyeSZuYnNwOyANCjxCUj4mbmJzcDtVbml2ZXJzaXR5IG9m IFdlc3Rlcm4gT250YXJpbzxCUj4mbmJzcDtMb25kb24sIE9udGFyaW8sJm5ic3A7IA0KQ2FuYWRh PEJSPiZuYnNwO042QSA1Qjc8L0ZPTlQ+PC9ESVY+DQo8RElWPiZuYnNwOzwvRElWPg0KPERJVj48 Rk9OVCBmYWNlPUFyaWFsIHNpemU9Mj4mbmJzcDtwaG9uZTogKDUxOSktNjYxLTIxMTEgZXh0LiAN Cjg2MzUzJm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5i c3A7IA0KPEJSPiZuYnNwO2ZheDombmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsgDQooNTE5 KS02NjEtMzAyMjxCUj4mbmJzcDtlbWFpbDombmJzcDsgPEEgDQpocmVmPSJtYWlsdG86c2RlY2tl ckB1d28uY2EiPnNkZWNrZXJAdXdvLmNhPC9BPjxCUj5fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fPEJSPjwvRk9OVD48L0RJVj48L0JPRFk+PC9IVE1MPg0K --0__=C1256BDF00572D258f9e8a93df938690918cC1256BDF00572D25-- From chemistry-request@server.ccl.net Fri Jun 21 23:51:11 2002 Received: from jingxian.xmu.edu.cn ([210.34.0.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5M3pAa25563 for ; Fri, 21 Jun 2002 23:51:10 -0400 Received: from zjcao ([210.34.15.230]) (authenticated bits=0) by jingxian.xmu.edu.cn (8.12.2/8.12.2) with ESMTP id g5M3vIaT009874 for ; Sat, 22 Jun 2002 11:57:19 +0800 (CST) Message-ID: <002301c2199f$e915a700$e60f22d2@zjcao> From: "zjcao" To: Subject: The calculation of solvation free energy Date: Sat, 22 Jun 2002 11:50:11 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g5M3pBa25564 Dear all, The free energy of solvation is the key parameter in describing solvation. Would you please to teach me how to calculate it for several solvation models, e.g. Onsager model, PCM model and discrete-continuum model? References are invited too. Thanks in advance! ZJ Cao