From chemistry-request@server.ccl.net Mon Jan 22 03:29:53 2001 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0M8Tnd05200 for ; Mon, 22 Jan 2001 03:29:51 -0500 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id OAA63635 for ; Mon, 22 Jan 2001 14:07:27 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id OAA28114 for ; Mon, 22 Jan 2001 14:06:01 +0530 Date: Mon, 22 Jan 2001 14:06:01 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: chemistry@ccl.net Subject: Summary: AIM analysis & ECP basis set In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Here is my query followed by the replies I got for this. Thanks for the useful replies. Tapan On Tue, 9 Jan 2001, Dr.Tapan K.Ghanty wrote: > Hi All, > > I was wondering whether Bader's Atom-in-Molecule (AIM) analysis > can be performed (in-principle as well as in-practice) on a > wavefunction which is calculated using ECP basis sets. > > With thanks, > > Tapan K. Ghanty REPLIES: ********* # 1 ------------------------------------------------------------------------ From: Frederick P. Arnold Jr. Sort of. You need to look up some papers by Gernot Frenking from around 1995 on this topic. The shortcomings basically are that because of the lack of core density, (1) spurious critical points appear in the molecular graph, (2) residual density in the core region caused by the s-orbitals causes numerical instabilities in various search routines, and (3) the first two make it difficult to reliably integrate the density, especially in regions of complex topology. You're probably better off doing everything up to the AIM analysis with ECP, and then using the basis sets in the Huzinaga green book (appropriately split and augmented) for a single-point calculation to generate the wfn file. -fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu # 2 -------------------------------------------------------------------- From: "Shobe, Dave" My understanding is that it can be done, IF one fills in the missing electron density. I've seen a paper somewhere where this was done, i.e. a fixed core density was added to the electron density from the calculation. I don't remember how they got the core density though, or anything helpful regarding tracking down the paper. :-( ("I don't remember the author or title, but I think the book was red.") From chemistry-request@server.ccl.net Mon Jan 22 07:18:21 2001 Received: from nikias.cc.uoa.gr (nikias.cc.uoa.gr [195.134.68.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MCIKd06967 for ; Mon, 22 Jan 2001 07:18:21 -0500 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id OAA16434 for ; Mon, 22 Jan 2001 14:18:09 +0200 (EET) Date: Mon, 22 Jan 2001 14:18:09 +0200 (EET) From: Ioannis Kerkines To: chemistry@ccl.net Subject: Free MM3 programs for WinME? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear listmembers, Can anybody advise me of any free Win95/98/ME programs which can perform MM3 calculations? Thanks in advance, I will summarize. Ioannis From chemistry-request@server.ccl.net Mon Jan 22 03:41:01 2001 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0M8f0d05262 for ; Mon, 22 Jan 2001 03:41:01 -0500 Received: from dcu.ie (136.206.86.63) by hawk.dcu.ie (5.1.050) id 3A3F6BC300086E4B for chemistry@ccl.net; Mon, 22 Jan 2001 08:41:54 +0000 Message-ID: <3A6BF262.64723463@dcu.ie> Date: Mon, 22 Jan 2001 08:42:11 +0000 From: Dermot Brougham X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary:molecular modelling workshop Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A couple of weeks ago I asked a question about running a molecular modelling workshop, thanks to all who replied. The original question and summary are below. Sorry about the delay Original question: >I am currently applying for funding to run a workshop in molecular >modelling for our 4th year group (40 students). I plan to give 4-5 >lectures and then have a series of workshops (maybe 4x3 hours) with >progressively less supervision as time goes on. Ending up with the >students picking a problem of their own (probably from their organic >chemistry lectures) and tackling it using whatever methods they see as >fit and then writing a short report. Maybe the people who read the CCL >have done something similar. I would be grateful for any advice, >particularly about: >Software: Best? Value for money? >Hardware: Do you need a PC each or can you have them in pairs, >threes....? >Pedagogy: >Has there been much published on this type of course? >What are the major issues? > Does the course I have outlined make pedagogical >sense? >Or is there a superior alternative approach? Replies: The consensus is that Spartan is the best software Andreas Ehlers replied "It provides a very good GUI and contains all the methods from MM, semi empirical to ab initio, so the students don't have to change programs and write specific inputs for each problem. But it is expensive." Yes cost is the problem here, several others agreed with Andreas. Among the free options were MOE, recommended by David ENOT "Recently, I ve seen a demonstration of MOE which seems to be advantageous : you can perform classical modeling tasks as well as drug design in a highly pedagogical way, all the platforms are supported and it's free for education. Have a look at http://www.chemcomp.com " I haven't had a chance to try it yet. Also free is WebMolecules Over 200,000 Molecular Models Online in Full 3D http://www.webmolecules.com Requires 3D plug-in. Indexed and searchable. Although this isn't quite what I was looking for myeself! For a little more money: Molecules-3D 3D Molecular Model Building http://www.molecules.com/m3d25int.shtml Great for new students. Only $49 Molecules-3D Pro 3D Molecular Modelling http://www.molecules.com/m3d25int.shtml Ideal for students interested in Computational Chemistry. $99 As recommended by John Vermeer Several people from MSI contacted me talking about Materials Studio "http://staging.msi.com/materials/studio/ Or if you wish to evaluate a copy of Materials Visualizer: http://staging.msi.com/materials/studio/quote/" I have yet to try this! Several respondants recommended third party individuals who have run workshops, I am in the process of contacting these people, I won't give their names as they haven't replied yet. But if they throw up any nuggets I will inform the CCL. In terms of pedagogy there appears to be many ways to teach MM successfully, thanks to Hens Borkent, Michael Nolan and others here. Most replies suggested that what I had outlined will work, but that it is very important to keep the groups small (stagger the sessions if necessary). People disagreed as to whether one or two per PC is best, probably two if the students are "general chemists". It was agreed that you should never have more than two per PC and also that the course should be short if it is for general chemistry, i.e. 2 or at most 3 weeks. What Hens said was good: He uses "a web interface to mopac calculations, based on the Chime plugin, as you can find under http://www.cmbi.kun.nl/wetche/organic/ It requires W95/98 Netscape 4.5 - 4.7 to function properly, in particular the 'editor'. On the editor page you will also find suggestions for exercises. Since this is not really a modelling course, a number of input files have been constructed beforehand, and the students simply submit them, but they can also edit the files if they want to. On practical questions: We prefer them to work in pairs, which forces them to discuss the subject among eachother, talk about it. Three people with one mouse is too many. It is nice indeed to have a goal in the end: either a kind of competition, who comes up with the best figures, lowest minimum, etc., or a presentation, in Powerpoint or HTML (chime), as you propose. It is also our experience that courses of this type should not take too long. There should be regular interrupts, classical lectures etc, otherwise they start "playing" with the computer, chatting, e-mail, browsing. The main goal is to keep them interested in the subject, add the right amount of interactivity to keep them busy for a while, then have a break and get the group together in a discussion of the results. Sometimes you have luck if you ask them to suggest their own problems, but it is wise to have some problems at hand. I noticed that many organic chemists work on very large molecules these days, biological or supra- molecular, that are not so easy to model." One follow up question, I was expecting that Tinker would be mentioned, but it wasn't; Tinker is free; is it any good? Easy for students? GUI? Thanks again Dermot -- Dr. Dermot Brougham, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland. Tel: 353 1 7005472 Fax: 353 1 7005503 From chemistry-request@server.ccl.net Mon Jan 22 08:17:12 2001 Received: from ncsbex72.ncsbe.jnj.com (smtp.be.jnj.com [194.74.108.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MDHBd07117 for ; Mon, 22 Jan 2001 08:17:11 -0500 Received: from smtp.jnj.com by smtp.jnj.com id f0MDHBq06919; Mon, 22 Jan 2001 14:17:11 +0100 (MET) Received: FROM ncsbebeexh33.ncsbe.jnj.com BY ncsbebesvc06.jnjeu.jnj.com ; Mon Jan 22 14:17:10 2001 +0100 Received: by ncsbebeexc1.ncsbe.jnj.com with Internet Mail Service (5.5.2650.21) id ; Mon, 22 Jan 2001 14:17:10 +0100 Message-ID: <3C843A61C1C6D4119E0A0008C7242D3ED33EC0@JANBEBEEXS3.janbe.jnj.com> From: "Bultinck, Patrick [JanBe Extern]" To: "'chemistry@ccl.net'" Subject: Generating atomic charges (non q-chemical) Date: Mon, 22 Jan 2001 14:17:08 +0100 Dear, Could anybody point me to information on the most commonly used schemes for generating atomic charges for molecules, using non-quantumchemical methods. The goal is to obtain charges on atoms FAST, as is done in many molecular modelling force-field calculations. If possible, please include in which software packages these methods have been implemented. A summary will be sent to other interested subscribers. Thanks, Patrick Bultinck, Ghent University, Belgium (currently post-doc with Janssen Research Foundation, Belgium) From chemistry-request@server.ccl.net Mon Jan 22 08:31:03 2001 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MDV2d07193 for ; Mon, 22 Jan 2001 08:31:02 -0500 Received: from cedar-f.csc.fi (cedar.csc.fi [128.214.248.26]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id PAA20065 for ; Mon, 22 Jan 2001 15:31:01 +0200 Date: Mon, 22 Jan 2001 15:31:00 +0200 From: Maija Lahtela To: chemistry@ccl.net Subject: Visualization of double and triple bonds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would like to know if there are molecular modeling program such as RasMol, WebLAbviewer that could present double bond as two tubes and triple bond with three tubes ( the way as student are used books of chemistry in high school or collage). Yours, Maija L.-K. ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela@csc.fi, Internet:www.csc.fi **************************************************** From chemistry-request@server.ccl.net Mon Jan 22 08:56:19 2001 Received: from mail1.doit.wisc.edu (mail1.doit.wisc.edu [144.92.9.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MDuJd07474 for ; Mon, 22 Jan 2001 08:56:19 -0500 Received: from [128.104.71.140] by mail1.doit.wisc.edu id HAA224136 (8.9.1/50); Mon, 22 Jan 2001 07:56:19 -0600 Message-Id: <200101221356.HAA224136@mail1.doit.wisc.edu> From: uddin@chem.wisc.edu To: CHEMISTRY@ccl.net Date: Mon, 22 Jan 2001 07:53:26 -0600 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Electronic ground state configuration for transition metals CC: uddin@chem.wisc.edu X-Confirm-Reading-To: uddin@chem.wisc.edu X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12b) Hello, I am trying to calculate the energy of some transition metals and small metal complexes using gaussian and jaguar programs. In some cases, the difficulty is to find the atomic electronic ground state configuration (such as d^n or d^(n-1)s^1/d^(n-2)s^2) and the electronic configuration used by metal in the complex. Is there any option in either gaussian98 or Jaguar to determine which configuration is used or can I force a specific configuration to be used in the calculation? I would appreciate your help. Thank you Regards, Jamal Uddin From chemistry-request@server.ccl.net Mon Jan 22 10:41:32 2001 Received: from hamilton.edu (ruby.hamilton.edu [150.209.8.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MFfVd08020 for ; Mon, 22 Jan 2001 10:41:31 -0500 Received: from [150.209.87.102] (Julius.hamilton.edu [150.209.87.102]) by hamilton.edu (8.9.3/8.9.3) with SMTP id KAA16868 for ; Mon, 22 Jan 2001 10:42:08 -0500 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Mon, 22 Jan 2001 10:38:16 -0500 To: chemistry@ccl.net From: Steven Feldgus Subject: New CCSD/ONIOM question Hi, First off, I'd like to thank everyone who enlightened me about the use of numerical gradients in CCSD in G98, hence the limit in the number of variables. However, I'm actually trying to do an ONIOM calculation on a 54-variable system, with CCSD(T) on a small portion of that molecule. I still have the 50-variable limit. In the manual, Gaussian mentions that when numerical frequencies are required on any one portion of the molecule, they will be used on the entire molecule. Does that hold for gradients in geometry optimizations as well? Thanks, Steve Feldgus Hamilton College From chemistry-request@server.ccl.net Mon Jan 22 12:59:33 2001 Received: from server5.safepages.com ([216.127.146.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MHxWd08785 for ; Mon, 22 Jan 2001 12:59:32 -0500 Received: from kressj (5131-196-251.008.popsite.net [209.69.196.251]) by server5.safepages.com (Postfix) with SMTP id 87FBD7099C; Mon, 22 Jan 2001 17:59:10 +0000 (GMT) Message-ID: <001501c0849d$08c47ac0$0100a8c0@webrise.net> From: "Jim Kress" To: "Ioannis Kerkines" , References: Subject: Re: CCL:Free MM3 programs for WinME? Date: Mon, 22 Jan 2001 12:59:13 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Tinker. http://dasher.wustl.edu/tinker/ Jim ----- Original Message ----- From: "Ioannis Kerkines" To: Sent: Monday, January 22, 2001 7:18 AM Subject: CCL:Free MM3 programs for WinME? > Dear listmembers, > > Can anybody advise me of any free Win95/98/ME programs which can perform > MM3 calculations? > > Thanks in advance, I will summarize. > > Ioannis > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon Jan 22 09:50:03 2001 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MEo2d07769 for ; Mon, 22 Jan 2001 09:50:02 -0500 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Mon, 22 Jan 2001 14:49:48 +0000 Sender: mb@ucl.ac.uk Message-ID: <3A6C4894.4F214B49@ucl.ac.uk> Date: Mon, 22 Jan 2001 14:49:56 +0000 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "Bultinck, Patrick [JanBe Extern]" CC: "'chemistry@ccl.net'" Subject: Re: CCL:Generating atomic charges (non q-chemical) References: <3C843A61C1C6D4119E0A0008C7242D3ED33EC0@JANBEBEEXS3.janbe.jnj.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Bultinck, Patrick [JanBe Extern]" wrote: > > Dear, > > Could anybody point me to information on the most commonly used schemes for > generating atomic charges for molecules, using non-quantumchemical methods. > The goal is to obtain charges on atoms FAST, as is done in many molecular > modelling force-field calculations. If possible, please include in which > software packages these methods have been implemented. A summary will be > sent to other interested subscribers. > > Thanks, > > Patrick Bultinck, Ghent University, Belgium > (currently post-doc with Janssen Research Foundation, Belgium) > i see two ways: 1) you use one of the common MD-packages like CHARMM or AMBER. usually these programs include predetermined partial-charges for many sorts of residues (mainly biomolecular) 2) you use algorithms like charge equilibration (J. Phys. Chem., 95, 3358 (1991)) or the gasteiger method (Tetrahedron, 36, 3219 (1980)) however -- i don't know what sort of calculations you do -- but in my humble opinion these methods usually give partial charges of (at the least) questionable quality ... mic =================================================== Debug is human, de-fix divine. --------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk, http://www.ucl.ac.uk/~uccambr/ --------------------------------------------------- From chemistry-request@server.ccl.net Mon Jan 22 11:47:38 2001 Received: from hotmail.com (f205.law8.hotmail.com [216.33.241.205]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MGlbd08438 for ; Mon, 22 Jan 2001 11:47:38 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 22 Jan 2001 08:45:37 -0800 Received: from 134.129.118.52 by lw8fd.law8.hotmail.msn.com with HTTP; Mon, 22 Jan 2001 16:45:37 GMT X-Originating-IP: [134.129.118.52] From: "xin hu" To: amber@cgl.ucsf.edu Cc: chemistry@ccl.net Subject: question about RESP calculation Date: Mon, 22 Jan 2001 16:45:37 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 22 Jan 2001 16:45:37.0673 (UTC) FILETIME=[BF58BF90:01C08492] Hi, I am a newer for AMBER and just working on the resp charge fitting. Following the instruction I did the calaulation of water using Gamess(US) and run the script "run.resp", just as the example, but the result of charge is always zero: ----------------------------------------------- Restrained ESP Fit 2.3 Amber 4.1 ----------------------------------------------- TITLE ----------------------------------------------- inopt = 0 ioutopt = 0 nmol = 1 iqopt = 0 ihfree = 1 irstrnt = 1 iunits = 0 qwt = 0.00050000 wtmol(1) = 1.000000 subtitle: TITLE ich = 0 iuniq = 3 1 8 0 2 1 0 3 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ---------------------------------------------------------------------------- ATOM COORDINATES CHARGE X Y Z ---------------------------------------------------------------------- ---------------------------------------------------------------------- Charge on the molecule(ich) = 0 Total number of atoms (iuniq) = 3 Weight factor on initial charge restraints(qwt)= 0.50000E-03 there are 3 charge constraints: 1 0 0 1 2 0 0 1 3 0 0 1 Reading esp"s for molecule 1 total number of atoms = 3 total number of esp points = 34 center X Y Z 1 -0.5520723E+00 0.2380678E-01 0.0000000E+00 2 -0.4900439E+00 0.1812906E+01 0.0000000E+00 3 0.1155385E+01 -0.5140756E+00 0.0000000E+00 Initial ssvpot = 0.649 Number of unique UNfrozen centers= 3 Non-linear optimization requested. qchnge = nan qchnge = nan qchnge = nan Convergence in 2 iterations TITLE Point Charges Before & After Optimization no. At.no. q(init) q(opt) ivary d(rstr)/dq 1 8 0.000000 nan 0 nan 2 1 0.000000 nan 0 0.000000 3 1 0.000000 nan 0 0.000000 Sum over the calculated charges: nan Statistics of the fitting: The initial sum of squares (ssvpot) 0.649 The residual sum of squares (chipot) nan The std err of estimate (sqrt(chipot/N)) nan ESP relative RMS (SQRT(chipot/ssvpot)) nan Center of Mass (Angst.): X = 0.00000 Y = 0.00000 Z = 0.00000 Dipole (Debye): X = nan Y = nan Z = nan Dipole Moment (Debye)= nan Quadrupole (Debye*Angst.): Qxx = nan QYY = nan QZZ = nan Qxy = nan QXZ = nan QYZ = nan I do not know what's the problem with it. Seems the script run.resp did not extract the proper information from the *.dat file to generate the correct esp.in file. The total number of esp points are only 34. I try other molecules, and the result is always the same as water, the total number of esp points is 34 and the charges are all nan. Would someone please figure out what is the problem? I appreciate your help very much! ---------------------------------------------------------- Xin Hu Department of Pharmaceutical Sciences College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298(office) 701-231-4193(home) 701-231-7781(Fax) E-mail: xin_hu@ndsu.nodak.edu xxh0541@hotmail.com Mail address: 236 E Court University Village Fargo, ND 58102 ---------------------------------------------------------- _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Mon Jan 22 16:36:47 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0MLald10182 for ; Mon, 22 Jan 2001 16:36:47 -0500 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA04848 for ; Mon, 22 Jan 2001 16:36:46 -0500 (EST) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id NAA26450 for ; Mon, 22 Jan 2001 13:40:35 -0800 (PST) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma026444; Mon, 22 Jan 01 13:40:29 -0800 Message-Id: <5.0.2.1.2.20010122132735.00a84cb0@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 22 Jan 2001 13:28:00 -0800 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:Visualization of double and triple bonds In-Reply-To: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_227389038==_.ALT" --=====================_227389038==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed MSI's ViewerLite at: http://www.msi.com/life/products/weblab/viewer/ does this quite nicely. DG At 03:31 PM 1/22/01 +0200, you wrote: >Dear CCLers, > >I would like to >know if there are molecular modeling program such as RasMol, >WebLAbviewer that could present double bond as two tubes and triple bond >with three tubes ( the way as student are used books of chemistry in high >school or collage). > >Yours, >Maija L.-K. > >***************************************************** >Maija Lahtela-Kakkonen, Researcher >CSC-Scientific Computing >Tekniikantie 15 a D, P.O.Box 405 >FIN-02101 ESPOO FINLAND >TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 >E-MAIL mlahtela@csc.fi, Internet:www.csc.fi >**************************************************** > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --=====================_227389038==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MSI's ViewerLite at:
http://www.msi.com/life/products/weblab/viewer/
does this quite nicely.
DG


At 03:31 PM 1/22/01 +0200, you wrote:
Dear CCLers,

I would like to
know if there are molecular modeling program such as RasMol,
WebLAbviewer that could present double bond as two tubes and triple bond
with three tubes ( the way as student are used books of chemistry in high
school or collage).

Yours,
Maija L.-K.

*****************************************************
Maija Lahtela-Kakkonen, Researcher
CSC-Scientific Computing
Tekniikantie 15 a D, P.O.Box 405
FIN-02101 ESPOO  FINLAND
TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302
E-MAIL mlahtela@csc.fi, Internet:www.csc.fi
****************************************************



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--=====================_227389038==_.ALT-- From chemistry-request@server.ccl.net Mon Jan 22 19:33:55 2001 Received: from comm2.umaryland.edu (comm2.umaryland.edu [134.192.1.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0N0Xsd10925 for ; Mon, 22 Jan 2001 19:33:55 -0500 Received: from umaryland.edu (falcon2.umaryland.edu [134.192.68.11]) by comm2.umaryland.edu (8.9.3/8.9.3) with ESMTP id TAA14886 for ; Mon, 22 Jan 2001 19:33:55 -0500 (EST) Received: from localhost (nbanaval@localhost) by umaryland.edu (8.10.0/8.10.0) with ESMTP id f0N0QVZ29510 for ; Mon, 22 Jan 2001 19:26:31 -0500 (EST) Date: Mon, 22 Jan 2001 19:26:31 -0500 (EST) From: Nilesh Banavali To: chemistry@ccl.net Subject: WHAM programs for 1D PMF Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, Are there any stand-alone Weighted Histogram Analysis Method (WHAM) programs available out there to calculate a one-dimensional potential of mean force (PMF) given sampled values of a given reaction coordinate obtained by a set of constrained MD simulations. The program that I currently have access to is the one written by Bockzo and Brooks. The purpose of this inquiry is for me to personally understand empirically if the PMF calculated by different programs are different for the same set of coordinate values and if so why. I guess they should theoretically be the same, however, any help provided is greatly appreciated. I will summarize the responses. Thanks, Nilesh. ------------------------------------------------------------------------- NILESH BANAVALI GRADUATE STUDENT UNIVERSITY OF MARYLAND, BALTIMORE -------------------------------------------------------------------------