From chemistry-request@server.ccl.net Thu Feb 20 06:43:38 2003 Received: from Clarion.ucd.ie ([137.43.1.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1KBhcI09366 for ; Thu, 20 Feb 2003 06:43:38 -0500 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Clarion.ucd.ie by Clarion.ucd.ie (PMDF V6.2 #30697) id <0HAL00H01V8P2X@Clarion.ucd.ie> for chemistry@ccl.net; Thu, 20 Feb 2003 11:43:37 +0000 (GMT) Received: from noelfitz6 (noelfitz6.ucd.ie [137.43.24.17]) by Clarion.ucd.ie (PMDF V6.2 #30697) with ESMTP id <0HAL00G8RV8P7E@Clarion.ucd.ie>; Thu, 20 Feb 2003 11:43:37 +0000 (GMT) Date: Thu, 20 Feb 2003 11:41:04 +0000 From: Laurence Cuffe Subject: Re: CCL:RMS Force and Maximum displacement In-reply-to: <001e01c2d6c5$b21a61d0$340510ac@ismmm.edu.cu> To: "MSc. Alexis Otero Calvi" , chemistry@ccl.net Message-id: <3E54BED0.21092.1000ECF3@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal On 17 Feb 2003, at 15:46, MSc. Alexis Otero Calvi wrote: >Hello all, >We are perform the B3LYP calculation for transition metal complex with 6-31G(d) basis set for C, H, P, S and LanL2DZ with ECP for Ni. > >The result: > > Item Value Threshold Converged? > Maximum Force 0.000003 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.003540 0.001800 NO > RMS Displacement 0.001065 0.001200 YES > Predicted change in Energy=-2.171072D-08 > Optimization completed on the basis of negligible forces. > -- Stationary point found. > >How I can solve the problem with the RMS Force and Maximum Displacement convergence. > This isn't a problem. Your molecule has a very shallow minimum hence the displacement figures are still quite large, however the forces are negligible hence the program decided that it is at a minima. All the best Laurence Cuffe >Alexis > > > > > > From chemistry-request@server.ccl.net Thu Feb 20 06:28:59 2003 Received: from oulu.fi ([130.231.240.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1KBSwI09055 for ; Thu, 20 Feb 2003 06:28:59 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id NAA14998; Thu, 20 Feb 2003 13:28:42 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id NAA00610; Thu, 20 Feb 2003 13:28:41 +0200 (EET) Date: Thu, 20 Feb 2003 13:28:41 +0200 (EET) From: =?ISO-8859-1?Q?Atte_Sillanp=E4=E4?= X-X-Sender: asillanp@paju.oulu.fi Reply-To: atte.sillanpaa@oulu.fi To: Phil Hultin cc: Computational Chemistry List Subject: Re: CCL:Results (Was: Gaussian "Alter" Keyword) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 19 Feb 2003, Phil Hultin wrote: > I was interested by the recent question about performing a calculation on a > high-spin Fe(II) complex. I don't have any "technical" advice to offer as > to how to get the calculation to work - that has already appeared on CCL. > What caught my eye was the following: > "Unfortunately the results I obtain even with the small system are hardly > believable. The frontier orbitals do not resemble d orbitals very much and > the spin density is not concentrated on iron (only 1/4 of it is on Fe)." > > The quality of the calculation may well be suspect, owing to the problems in > converging, but is it really appropriate to judge the performance of a > computation by how closely it reproduces the qualitative pictures we use in > introducing undergraduates to electronic structure theory? In most cases > that I have examined, the HOMO and LUMO do not resemble hydrogen-like atomic > orbitals, nor would I expect them to. These are, after all, MOLECULAR > orbital calculations. The symmetry properties of these frontier orbitals > obey certain rules, but I don't know of any reason to expect them to look > very much like traditional pictures of atomic orbitals. > > I also wonder if the fact that spin density given by the reported > calculation is not concentrated where we would draw it on paper is all that > significant. After all, although in organic chemistry we tend to draw > methyl cation (CH3+) with the charge on carbon, calculations and other data > suggest that in fact the bulk of the charge is on the hydrogens. > > Most experimentalists use models that are only rough approximations to > reality - I include myself in that group, since I am primarily a synthetic > organic chemist. But, isn't at least part of the point of doing ab initio > calculations to find out more about what may be going on "under the hood" in > chemical structures? > > What do people think about the relationship between simple qualitative > models, more sophisticated ab initio models, and "reality" (whatever that > may be)? Well, I have no ultimate answer to what reality is, but what about spectroscopy? If we can rationalise the electronic transitions using the symmetries of the metal d-orbitals and selection rules, does that constitute proof for the actual electron configuration of the 'real' system to at least obey that symmetry? Could the validity of the computed electronic states be checked against the spectra they would produce by. e.g. a TDDFT calculation? I have also often found the calculated d-orbitals not to be the text-book-type, but as the 'real' (in this context stands for the optimised structure :) complexes or molecules seldom have high symmetry, I have not worried too much about it. Cheers, Atte atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Thu Feb 20 03:45:56 2003 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K8jtI26401 for ; Thu, 20 Feb 2003 03:45:55 -0500 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id MAA94019; Wed, 19 Feb 2003 12:55:01 +0100 (CET) Date: Wed, 19 Feb 2003 12:55:01 +0100 (CET) Message-Id: <200302191155.MAA94019@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: maharan@chem.univ.gda.pl CC: chemistry@ccl.net In-reply-to: (message from Maciej Haranczyk on Wed, 19 Feb 2003 15:33:20 +0100 (CET)) Subject: Re: CCL:ploting electron holes References: Hello, here are some hints. Compute (using Gaussian) a cube file with the electron density for each of the two species. Then compute a new cube file of the electron density difference with the cubman utility that comes with Gaussian. Finally use a program, that can calculate and visualize an isosurface of those cube data, for example OpenDX (an import filter is publicly available), gOpenMol or (try that first) Molekel. Regards, Ingo > Date: Wed, 19 Feb 2003 15:33:20 +0100 (CET) > From: Maciej Haranczyk > Content-Type: TEXT/PLAIN; charset=US-ASCII > Sender: "Computational Chemistry List" > Precedence: bulk > > Hello CCL, > > I would like to plot an electron hole (difference in electron density of > neutral and cation at the same geometry) from Gaussian98 outputs. Do you > know any software that can draw 2D or 3D picutes of electron holes ? > > Best wishes > Maciek > > > -- > > Maciek Haranczyk > maharan@chem.univ.gda.pl From chemistry-request@server.ccl.net Thu Feb 20 04:30:15 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K9UCI07311 for ; Thu, 20 Feb 2003 04:30:15 -0500 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 20 Feb 2003 10:29:58 +0100 Message-ID: <006001c2d8c2$dc544340$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: , References: <78DC4BAB.4AA9B6F0.0347FE40@netscape.net> Subject: Re: CCL:Babel For Windows Date: Thu, 20 Feb 2003 10:31:34 +0100 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 It seems to me that a bat file starts Babel in your case, its commands appear together with the response in the opening DOS window. The first command (C:\) already generates error instead of changing to drive c:. Very probably the backslash is not needed: the first command in the bat file should be "C:" instead of "C:\". Hope this helps Tamas E. Gunda -------------------------- Prof. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: To: Sent: Wednesday, February 19, 2003 20:05 Subject: CCL:Babel For Windows > Hi all > > I just reformatted my hard drive and installed WinXP and have just finished reinstalling all my software. > > I'm having a problem getting Babel for Windows to work though. > > I have Babel 1.6 in c:\babel16\babel16 and I have Babel 1.06 in c:\babel1.06. When I try and run Babel, by clicking on Go, I get the > following message in the DOS window... > > > F:\research\TS\pna>C:\ > 'C:\' is not recognized as an internal or external command, > operable program or batch file. > > F:\research\TS\pna>cd C:\babel16\babel16 > > F:\research\TS\pna>babel -ipdb "F:\research\TS\pna\pnaoctamerwithadenine.pdb" -o > xyz "F:\research\TS\pna\output.xyz" > 'babel' is not recognized as an internal or external command, > operable program or batch file. > > F:\research\TS\pna>pause > Press any key to continue . . . > > Yet if I try either babel at a command prompt, it works. I also have WinXP on my desktop at home and it works fine. > > Please respond to me at this address with any suggestions that you may have as i am not subscribed through this address. > > Thanks in advance, > > Richard Wood, Ph. D. > > > __________________________________________________________________ > The NEW Netscape 7.0 browser is now available. Upgrade now! http://channels.netscape.com/ns/browsers/download.jsp > > Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Feb 20 07:12:20 2003 Received: from mail-a.bcc.ac.uk ([144.82.100.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1KCCKI09853 for ; Thu, 20 Feb 2003 07:12:20 -0500 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 20 Feb 2003 12:12:17 +0000 Sender: mb@ucl.ac.uk Message-ID: <3E54C35F.1F4D8F22@ucl.ac.uk> Date: Thu, 20 Feb 2003 12:00:31 +0000 From: M Brunsteiner Organization: UCL X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: system size and pressure correlations in MD References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit dear all, I am looking for information on pressure correlations in liquds. If I did a molecular dynamics simulation, how would the size of the pressure fluctuations depend on the system size (the box-size in an MD simulation) and what would the spatial correlation function of the pressure as, e.g., calculated in subvolumes of the system look like ? What is the magnitude of the pressure fluctuations in a simple liquid or in a not so simple one as, e.g., water, as a function of the system size, what is the wave-length of these fluctuations (i.e. what is the time span between a pressure minimum and maxiumum in a given subvolume) and how far do they extend throughout the liquid? Any information/references are appreachiated. cheers! Michael ========================================================================== "Emotions are alien to me. I'm a scientist." (Spock, "This Side of Paradise", stardate 3417.3) -------------------------------------------------------------------------- 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 Thu Feb 20 05:48:24 2003 Received: from dove2.cf.ac.uk ([131.251.1.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1KAmNI08559 for ; Thu, 20 Feb 2003 05:48:23 -0500 Received: from maincf2p.cf.ac.uk ([131.251.4.71] helo=MAINCF2P) by dove2.cf.ac.uk with esmtp (Exim 4.05) id 18loFc-00052x-00 for chemistry@ccl.net; Thu, 20 Feb 2003 10:48:24 +0000 Received: from cardiff.ac.uk (m114.phrm.cf.ac.uk [131.251.35.246]) by MAINCF2P; Thu, 20 Feb 2003 10:48:13 +0000 Date: Thu, 20 Feb 2003 10:47:30 +0000 Subject: Re: CCL:Babel For Windows Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v546) From: Dimitrios Vlachakis To: chemistry@ccl.net Content-Transfer-Encoding: 7bit In-Reply-To: <78DC4BAB.4AA9B6F0.0347FE40@netscape.net> Message-Id: X-Mailer: Apple Mail (2.546) Dear Richard, I think the problem is that WinBabel cannot pickup the "babel files" on your pc just because they are in the wrong location. Try losing the second babel16 folder from your computer. So, put all the babel files in C:\babel16 I think that WinBabel is expecting the "babel files" to be in that directory only! hope that helps, Dimitrios Vlachakis PhD student, Cardiff University On Wednesday, February 19, 2003, at 07:05 pm, rlw987654@netscape.net wrote: > Hi all > > I just reformatted my hard drive and installed WinXP and have just > finished reinstalling all my software. > > I'm having a problem getting Babel for Windows to work though. > > I have Babel 1.6 in c:\babel16\babel16 and I have Babel 1.06 in > c:\babel1.06. When I try and run Babel, by clicking on Go, I get the > following message in the DOS window... > > > F:\research\TS\pna>C:\ > 'C:\' is not recognized as an internal or external command, > operable program or batch file. > > F:\research\TS\pna>cd C:\babel16\babel16 > > F:\research\TS\pna>babel -ipdb > "F:\research\TS\pna\pnaoctamerwithadenine.pdb" -o > xyz "F:\research\TS\pna\output.xyz" > 'babel' is not recognized as an internal or external command, > operable program or batch file. > > F:\research\TS\pna>pause > Press any key to continue . . . > > Yet if I try either babel at a command prompt, it works. I also have > WinXP on my desktop at home and it works fine. > > Please respond to me at this address with any suggestions that you may > have as i am not subscribed through this address. > > Thanks in advance, > > Richard Wood, Ph. D. > > > __________________________________________________________________ > The NEW Netscape 7.0 browser is now available. Upgrade now! > http://channels.netscape.com/ns/browsers/download.jsp > > Get your own FREE, personal Netscape Mail account today at > http://webmail.netscape.com/ > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Feb 20 01:51:54 2003 Received: from orion.lunarpages.com ([64.235.234.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K6prI24379 for ; Thu, 20 Feb 2003 01:51:53 -0500 Received: from adsl62-0-137-lns-p37.adsl.netvision.net.il ([62.0.137.37] helo=TESTING) by orion.lunarpages.com with esmtp (Exim 3.36 #1) id 18lkZC-0003gm-00; Wed, 19 Feb 2003 22:52:22 -0800 From: "Elie Cohen" To: "=?windows-1255?B?J7HowOW56Cc=?=" , Subject: RE: 2D to 3D converter Date: Thu, 20 Feb 2003 08:51:35 +0200 Message-ID: <003501c2d8ac$880775c0$8907000a@TESTING> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0036_01C2D8BD.4B92B6C0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal In-Reply-To: <000201c2d7de$62c822b0$7004facb@anakin> X-AntiAbuse: This header was added to track abuse, please include it with any abuse report X-AntiAbuse: Primary Hostname - orion.lunarpages.com X-AntiAbuse: Original Domain - ccl.net X-AntiAbuse: Originator/Caller UID/GID - [0 0] / [0 0] X-AntiAbuse: Sender Address Domain - drugdesign.org This is a multi-part message in MIME format. ------=_NextPart_000_0036_01C2D8BD.4B92B6C0 Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: quoted-printable Have a look to the site 'drugdesign.org' -> 3D databases Searching -> 2D-3D Converters =20 http://www.tripos.com/sciTech/inSilicoDisc/media/LITCTR/CONCORD.PDF =20 http://www.msg.ucsf.edu/local/programs/insightII/doc/life/insight2000.1/ converter/04_Method.html http://www2.chemie.uni-erlangen.de/software/corina/index.html =20 =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of =B1=E8=C0=E5=B9=E8 Sent: Wednesday, February 19, 2003 8:16 AM To: chemistry@ccl.net Subject: CCL:2D to 3D converter =20 Hi! =20 Is there any known freeware program converting 2D molecular structure to 3D for given sd or sdf files? =20 Any comment or information will be appreciated !! =20 Regards, =20 Jangbae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Jangbae Kim Researcher =20 Bio-Organic Science Division Korea Research Institute of Chemical Technology (KRICT) =20 P.O.Box 107, Yuseong, Taejeon, 305-600, Korea TEL : +82-42-860-7067 FAX : +82-42-861-0307 E-mail : jbkim@krict.re.kr * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * =20 ------=_NextPart_000_0036_01C2D8BD.4B92B6C0 Content-Type: text/html; charset="windows-1255" Content-Transfer-Encoding: quoted-printable

Have a look to the site = 'drugdesign.org' -> 3D databases Searching -> 2D-3D Converters

 

http://www.tripos.com/sciTech/inSilicoDisc/media/LITCTR/CO= NCORD.PDF

http://www.msg.ucsf.edu/local/programs/insightII/doc/life/= insight2000.1/converter/04_Method.html

http://www2.chemie.uni-erlangen.de/software/corina/index.h= tml

 

 

-----Original Message-----
From: Computational = Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of =B1=E8=C0=E5=B9=E8
Sent: Wednesday, February 19, = 2003 8:16 = AM
To: chemistry@ccl.net
Subject: CCL:2D to 3D = converter

 

Hi!

 

Is there any known freeware program converting 2D = molecular structure to 3D for given sd or sdf files?

 

Any comment or information will be appreciated = !!

 

Regards,

 

Jangbae

* * * * * * * * * * * * * * = * * * * * * * * * * * * * * * * * * * = *

Jangbae = Kim

Researcher           = ;            =             &= nbsp;           &n= bsp; 

Bio-Organic Science = Division

Korea Research Institute of = Chemical Technology (KRICT)

 

P.O.Box = 107,  Yuseong, = Taejeon,

305-600, = Korea

TEL : = +82-42-860-7067

FAX : = +82-42-861-0307

E-mail : = jbkim@krict.re.kr

* * * * * * * * * * * * * * = * * * * * * * * * * * * * * * * * * * = *

 

------=_NextPart_000_0036_01C2D8BD.4B92B6C0-- From chemistry-request@server.ccl.net Thu Feb 20 18:39:13 2003 Received: from telpacmail.tel-pacific.com ([203.88.255.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1KNdCI25830 for ; Thu, 20 Feb 2003 18:39:13 -0500 Received: from user (i088233226.rivernet.com.au [203.88.233.226]) by telpacmail.tel-pacific.com (8.11.6/8.11.6) with SMTP id h1KNd4q22536; Fri, 21 Feb 2003 10:39:05 +1100 Message-ID: <000401c2d939$46f9bb50$e2e958cb@user> Reply-To: "DrHuang.com" From: "DrHuang.com" To: "Jan Labanowski" Cc: References: Subject: Electrochemistry Software POLAROGRAPH.com 5.1 Date: Fri, 21 Feb 2003 10:39:11 +1100 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 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 I uploaded polar51.zip into ftp.ccl.net/incoming Electrochemistry Software POLAROGRAPH.com 5.1 Electrochemical simulation and data analysis DrHuang Pty Ltd 124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia Fax: (61 2) 9662 0516 mailto:info@electrochem.net info@DrHuang.com www.electrochem.net www.DrHuang.com www.electrochemistrySoftware.com Software POLAROGRAPH.com (former Polar) is virtual polarograph and general electrochemical simulator with data analysis. It analytically and digitally simulates voltammograms (polarograms) on virtually any mechanism (finite and semi-infinite diffusion and absorption) at over 10 electrode geometries (planar, spherical, semi-spherical, cylindrical, semi-cylindrical, microdisc, thin film, rotating disk, rotating ring electrodes) in over 10 techniques (linear sweep and CV, DC, normal pulse, reverse normal pulse, differential pulse, square wave, additive square wave, staircase voltammetries). It also simulates over 20 effect factors, e.g. charge current, resistance, noise, preconcentration time and potential, convection, pH, the reactant and product numbers, etc. User can type in his mechanism with any symbol. It also includes over 200 theoretical equations. It plots and analyses any x-y data for detecting peak location, peak value, semi-derivative, derivative, integral, semi-integral, convolution, deconvolution, curve fitting, and separating overlapped peaks and background current. www.Electrochem.Net www.ElectrochemistrySoftware.com