From chemistry-request@server.ccl.net Thu Jul 18 01:10:40 2002 Received: from sccrmhc01.attbi.com ([204.127.202.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6I5Aev19753 for ; Thu, 18 Jul 2002 01:10:40 -0400 Received: from C1353359A ([12.228.8.181]) by sccrmhc01.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020718051035.SZBH29588.sccrmhc01.attbi.com@C1353359A>; Thu, 18 Jul 2002 05:10:35 +0000 Reply-To: From: "Mark Thompson" To: Subject: Instructions for ArgusLab 3.0 -> 3.1 upgrade Date: Wed, 17 Jul 2002 22:12:02 -0700 Message-ID: <02d101c22e19$a6a4e640$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal Apologies for the continued bandwidth... We neglected to mention that the ArgusLab 3.1 upgrade is free to ArgusLab 3.0 users. The instructions for what to do are contained in the readme.txt file contained in the download. Basically, you simply uninstall your copy of ArgusLab 3.0 and install ArgusLab 3.1. Your eLicense should recognize 3.1 with no further effort on your part. Please send us email at "bugs@arguslab.com" if you have any problems. Cheers, Mark From chemistry-request@server.ccl.net Thu Jul 18 06:16:21 2002 Received: from mail.jadeinc.com ([209.57.24.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IAGLv24798 for ; Thu, 18 Jul 2002 06:16:21 -0400 Received: from igor.jadeinc.com [209.57.24.245] by mail.jadeinc.com with ESMTP (SMTPD32-6.06) id A51E1ACC0110; Thu, 18 Jul 2002 06:14:54 -0400 Message-Id: <5.1.1.6.2.20020718061716.00a048d0@jadeinc.com> X-Sender: smolnar@jadeinc.com X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 18 Jul 2002 06:22:58 -0400 To: Chemistry@ccl.net From: "Stephen P. Molnar, Ph.D." Subject: Problem with ADT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Clueless in Columbus - starting AutoDock Tools. I've installed complete1.5_i86Linux2_acad.tar.Z. When I start adt, after sourcing install.bash, I get the message: 'polygonOffset extension FAILED' I would assume this is a python error, as adt, seems to work,. but my question is what have I failed to install? I am running the SuSE v7.1 Linux distribution. Thanks in advance. From chemistry-request@server.ccl.net Thu Jul 18 03:05:52 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6I75pv21648 for ; Thu, 18 Jul 2002 03:05:51 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GZF00LGINPNPD@mailstudenti.unimi.it> for chemistry@ccl.net; Thu, 18 Jul 2002 09:05:47 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GZF00F5FNK18T@smtp.unimi.it> for chemistry@ccl.net; Thu, 18 Jul 2002 09:02:25 +0200 (MEST) Date: Thu, 18 Jul 2002 09:06:52 +0200 From: Giulio Vistoli Subject: Re: cartesian to pdb To: pdb-l@rcsb.org, chemistry@ccl.net Message-id: <001c01c22e29$b1761d40$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <20020717171204.48795.qmail@web13405.mail.yahoo.com> You can use our program VEGA (http://users.unimi.it/ddl) that can convert catesian coordinates in several file formats including pdb format Best regards Giulio Vistoli ----- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Thu Jul 18 08:32:18 2002 Received: from ultra3000.ifqsc.sc.usp.br ([143.107.228.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6ICWHv26888 for ; Thu, 18 Jul 2002 08:32:17 -0400 Received: from floyd (floyd.ifqsc.sc.usp.br [143.107.228.51]) by ultra3000.ifqsc.sc.usp.br (8.11.0/8.11.0) with SMTP id g6ICbCk17652; Thu, 18 Jul 2002 09:37:12 -0300 Message-ID: <002801c22e56$8f7b8fe0$33e46b8f@if.sc.usp.br> From: "Alexandre Suman de Araujo" To: "Paul Darwen" , References: Subject: Re: CCL:Problem with Kabsch measure for RMSD on planar molecules Date: Thu, 18 Jul 2002 09:28:02 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 I made a program that implement Kabsch algorithm in a visual windows program. It's free, but it's a beta version yet. If you want a copy, send me a e-mail and I'll send it to you... ok???!!! Alexandre Suman de Araujo IFSC - USP - São Carlos UIN: 6194055 ----- Original Message ----- From: "Paul Darwen" To: Sent: Wednesday, July 17, 2002 9:36 PM Subject: CCL:Problem with Kabsch measure for RMSD on planar molecules > > I have a problem with the Kabsch method of measuring root-mean-square > distance (RMSD) between molecules, as described in Kabsch 1978, Acta > Cryst A34:827-828. > > As far as I can make out, the Kabsch method works so long as three > or more planes are needed to intersect all the atoms. This means > that if a molecule happens to (say) be in a single flat plane, then > the Kabsch method chokes. > > For example, consider a molecule that's two carbon rings joined by > a bridge. This makes it flat. > > Below are two Sybyl2 copies of this molecule, but rotated and translated. > Their root-mean-square distance (RMSD) after alignment should be zero. > > But running Tinker's "superpose" program will align them lengthwise, > but they're still rotated about the lengthwise axis and not aligned. > The same thing happens in VMD if you try to align them with the script > /usr/local/lib/vmd/scripts/vmd/rmsd.tcl > Both of these incorrectly return an RMSD that's way more than zero. > > Has anyone written an RMSD measure that copes with planar molecules > like this? If you can run the following two molecules through your > align-and-measure-RMSD routine and get zero for an answer, I'd be > grateful for a copy. > > __________________________________________________________________ > > Paul Darwen www.protagonist.com.au/darwen > Protagonist Pty Ltd darwen@protagonist.com.au > Brisbane 4064 Australia Phone: +61-7-3377-0304 > > > --------------- This is the first of two molecules --------------- > > @MOLECULE > Bridge bond between two carbon rings > 22 23 1 > SMALL > NO_CHARGES > > @ATOM > 1 C1 1.304260 1.349055 -0.389125 C.2 > 2 C2 1.980455 0.216229 -0.145061 C.2 > 3 C3 1.892984 -0.380446 1.046579 C.2 > 4 C4 1.123138 0.166682 1.990862 C.2 > 5 C5 0.447667 1.299539 1.744975 C.2 > 6 C6 0.512887 1.932896 0.546310 C.2 > 7 H7 -0.161845 1.681260 2.577240 H > 8 H8 1.043615 -0.318373 2.979753 H > 9 H9 2.448954 -1.312367 1.248134 H > 10 H10 2.614125 -0.227590 -0.933089 H > 11 H11 1.432842 1.773440 -1.395729 H > 12 C12 -0.113409 3.725645 -0.903027 C.2 > 13 C13 -0.788738 4.858585 -1.148921 C.2 > 14 C14 -1.558584 5.405739 -0.204656 C.2 > 15 C15 -1.646220 4.808998 0.986939 C.2 > 16 C16 -0.970147 3.676100 1.230993 C.2 > 17 C17 -0.178748 3.092243 0.295605 C.2 > 18 H18 -1.098820 3.251664 2.237563 H > 19 H19 -2.279900 5.252856 1.774946 H > 20 H20 -2.114383 6.337763 -0.406164 H > 21 H21 -0.709092 5.343685 -2.137780 H > 22 H22 0.496097 3.343872 -1.735268 H > > @BOND > 1 1 2 1 > 2 1 6 1 > 3 1 11 1 > 4 2 3 1 > 5 2 10 1 > 6 3 4 1 > 7 3 9 1 > 8 4 5 1 > 9 4 8 1 > 10 5 6 1 > 11 5 7 1 > 12 6 17 1 > 13 12 13 1 > 14 12 17 1 > 15 12 22 1 > 16 13 14 1 > 17 13 21 1 > 18 14 15 1 > 19 14 20 1 > 20 15 16 1 > 21 15 19 1 > 22 16 17 1 > 23 16 18 1 > > @SUBSTRUCTURE > 1 **** 1 > > > --------------- This is the second of two molecules --------------- > > @MOLECULE > Bridge bond between two carbon rings > 22 23 1 > SMALL > NO_CHARGES > > @ATOM > 1 C1 0.054840 0.525138 -1.730657 C.2 > 2 C2 1.112013 -0.267815 -1.962393 C.2 > 3 C3 2.327386 0.082664 -1.533765 C.2 > 4 C4 2.474774 1.233137 -0.871667 C.2 > 5 C5 1.416448 2.024847 -0.640943 C.2 > 6 C6 0.167392 1.700650 -1.061558 C.2 > 7 H7 1.626775 2.952893 -0.089236 H > 8 H8 3.475262 1.532683 -0.512794 H > 9 H9 3.197548 -0.569107 -1.724045 H > 10 H10 0.978844 -1.216950 -2.510944 H > 11 H11 -0.908118 0.160964 -2.117910 H > 12 C12 -0.802543 3.687019 -0.155836 C.2 > 13 C13 -1.859722 4.479966 0.075891 C.2 > 14 C14 -3.075096 4.129477 -0.352705 C.2 > 15 C15 -3.222482 2.979014 -1.014814 C.2 > 16 C16 -2.164151 2.187340 -1.245587 C.2 > 17 C17 -0.915090 2.511520 -0.824932 C.2 > 18 H18 -2.374444 1.259272 -1.797273 H > 19 H19 -4.223035 2.679500 -1.373569 H > 20 H20 -3.945250 4.781258 -0.162414 H > 21 H21 -1.726500 5.429133 0.624380 H > 22 H22 0.160424 4.051217 0.231410 H > > @BOND > 1 1 2 1 > 2 1 6 1 > 3 1 11 1 > 4 2 3 1 > 5 2 10 1 > 6 3 4 1 > 7 3 9 1 > 8 4 5 1 > 9 4 8 1 > 10 5 6 1 > 11 5 7 1 > 12 6 17 1 > 13 12 13 1 > 14 12 17 1 > 15 12 22 1 > 16 13 14 1 > 17 13 21 1 > 18 14 15 1 > 19 14 20 1 > 20 15 16 1 > 21 15 19 1 > 22 16 17 1 > 23 16 18 1 > > @SUBSTRUCTURE > 1 **** 1 > > --------------- End of the second of two molecules --------------- > > > > -= 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 Jul 18 04:36:32 2002 Received: from angelo.kcl.ac.uk ([137.73.66.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6I8aVv23348 for ; Thu, 18 Jul 2002 04:36:31 -0400 Received: from kcl.ac.uk (pc205-29.pcy.kcl.ac.uk [137.73.205.29]) by angelo.kcl.ac.uk with ESMTP id g6I8Z4th014584; Thu, 18 Jul 2002 09:35:04 +0100 (BST) Message-ID: <3D3673CE.4B93F0EF@kcl.ac.uk> Date: Thu, 18 Jul 2002 08:52:46 +0100 From: SCT Organization: KCL X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: eric hu CC: chemistry@ccl.net, pdb-l@rcsb.org Subject: Re: CCL:cartesian to pdb References: <20020717171204.48795.qmail@web13405.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean hi eric, are you familiar with the program babel? it transforms various molecular visualization formats. you can read more and get it from this web site http://smog.com/chem/babel/ hope this helps sct eric hu wrote: > Hi, I wonder if there is an easy way to change the > cartesian coordinates to pdb format. Thanks! > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.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 Jul 18 10:28:13 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g6IESDd30421; Thu, 18 Jul 2002 10:28:13 -0400 Message-Id: <200207181428.g6IESDd30421@server.ccl.net> Subject: Re: Problem with Kabsch measure for RMSD on planar molecules Date: Thu, 18 Jul 2002 13:01:24 +0100 From: "Dr. Peter Bladon" To: Paul Darwen Cc: CHEMISTRY@ccl.net Dear Paul, I have adopted a different approach to the problem of aligning and/or comparing two structures. The approach is detailed in the paper: "A rapid method for comparing and matching the spherical parameter surfaces of molecules and other irregular objects" J. Mol. Graphics, 1989,7,130. The method is implemented in various forms in the Interchem suite of programs. In INTERCHEM (for SGI machines) or INTERCHEM-PC (for Windows machines) there was no problem in aligning your two structures. Although the rms residuals were not exactly zero the two structures overlaid pretty well. A more sever case would be exemplified by linear molecules such as acetylene. Again there was no problem. The software is available by following links from: http://www.interprobe.co.uk/inter/interprobe.html The software is free to academics but commercial enterprises are expected to pay a fee. Cheers Peter Bladon From chemistry-request@server.ccl.net Thu Jul 18 11:03:00 2002 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IF2xr31851 for ; Thu, 18 Jul 2002 11:03:00 -0400 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.4905); Thu, 18 Jul 2002 11:01:43 -0400 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Thu, 18 Jul 2002 11:04:17 -0400 Subject: A Perplexing AIM question From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 18 Jul 2002 15:01:43.0957 (UTC) FILETIME=[07A7AC50:01C22E6C] Hello all, As there has been a rash of AIM questions as of late, I'd like to add one more. If I take ethane and run a minimization of the structure at the RB3LYP/6-31G(d) level I obtain a perfectly nice structure as expected. I can take the Cartesian coordinates from the Gaussian output and create an XYZ file that can be read within several programs, including the free ViewerLite from Accelrys. All looks good, and I measure very reasonable C-C bond lengths of 1.53 A, C-H bond of 1.10 and a C-C-H angle of 111.4 (and I say all this just to prove I can create an XYZ file properly!). I then performed an AIM analysis on this structure within G98W (keywords: output=wfn punch=archive aim). Furthermore, I then took the wavefunction generated and subjected it to a calculation of its critical points in the (formerly free) program AIM2000. Both G98W and AIM2000 generated exactly the same Cartesian coordinates for the "attractors" and for the critical points on the attractor interaction lines. (ok: so I can perform an AIM calculation properly, too!) Finally, I simply lifted the cartesian coordinates from either of these two output files and created a new XYZ file (I use ghost atoms (Bq) to define the critical points). When I view the structure though, the C-C bond is now 2.89 A (!!) and the C-H bond 2.04 A but the C-C-H bond angle remains the same. (the same holds true if the Bq atoms are not included in the file). As the "attractors" are expected to simply be the atomic nuclei, why are the bond distances different from the minimized structure? The answer is not obvious to me. Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" From chemistry-request@server.ccl.net Thu Jul 18 11:59:19 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IFxJr00777 for ; Thu, 18 Jul 2002 11:59:19 -0400 Received: (from xiangjun@localhost) by rutchem.rutgers.edu (8.9.3/8.9.3) id LAA2733015; Thu, 18 Jul 2002 11:59:11 -0400 (EDT) Date: Thu, 18 Jul 2002 11:59:11 -0400 (EDT) Message-Id: <200207181559.LAA2733015@rutchem.rutgers.edu> From: Xiang Lu To: Paul Darwen CC: CHEMISTRY@ccl.net In-reply-to: <200207181428.g6IESDd30421@server.ccl.net> (cbas25@strath.ac.uk) Subject: Re: CCL:Problem with Kabsch measure for RMSD on planar molecules Reply-to: xiangjun@rutchem.rutgers.edu Dear Paul: Your problem arises because of the "non-equivalent" sequential numbering of atoms between the two structures. Using RasMol (with -mol2 option), and with "label %i" command, you will see the numbering of carbons atoms in your two structures as follows: 15-----16 05-----04 / \ / \ / \ / \ #1 14 17------06 03 \ / \ / \ / \ / 13-----12 01-----02 13-----12 05-----04 / \ / \ / \ / \ #2 14 17------06 03 \ / \ / \ / \ / 15-----16 01-----02 The RMSD (using only C atoms) is 1.3285 A. If you simply swap (12<--->16) and (13<--->15) in structure #2, you will get RMSD to be zeros, as you would expect. If you would like to know more about ls-fitting between two structures and ls-fitting of a plane to a set of atoms, with working examples, you might find the following URL helpful: http://rutchem.rutgers.edu/~olson/jmb/ls_fit.html Xiang-Jun -- Dr. Xiang-Jun Lu | Tel: (732) 445 4619 (O) Department of Chemistry | Rutgers University | Fax: (732) 445 5958 610 Taylor Road | Email: xiangjun@rutchem.rutgers.edu Piscataway, NJ 08854-8087 | URL: http://rutchem.rutgers.edu/~xiangjun/ From chemistry-request@server.ccl.net Thu Jul 18 12:22:10 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IGMAr01420 for ; Thu, 18 Jul 2002 12:22:10 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.4/8.12.4/Guy-23-01-2002) with ESMTP id g6IGM5TM002114; Thu, 18 Jul 2002 18:22:05 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id SAA23478; Thu, 18 Jul 2002 18:20:52 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3D36EA99.CC3E8325@lctn.uhp-nancy.fr> Date: Thu, 18 Jul 2002 18:19:37 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: Gary Breton CC: CHEMISTRY@ccl.net Subject: Re: CCL:A Perplexing AIM question References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Gary Breton wrote: > bond lengths of 1.53 A, C-H bond of 1.10 and a C-C-H angle of 111.4 (and I > say all this just to prove I can create an XYZ file properly!). > ... > the critical points). When I view the structure though, the C-C bond is now > 2.89 A (!!) and the C-H bond 2.04 A but the C-C-H bond angle remains the > same. (the same holds true if the Bq atoms are not included in the file). > > As the "attractors" are expected to simply be the atomic nuclei, why are the > bond distances different from the minimized structure? The answer is not > obvious to me. > > Gary W. Breton > Chair and Associate Professor > Department of Chemistry > Berry College > PO Box 495016 > Mount Berry, GA 30149 > > "There's a light at the > end of the tunnel, but it > may be an oncoming train" > > -= 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 What about the conversion of Angstrom to Bohr... 1 Bohr = 0.529177 Angstrom AIM2000 is working in a.u. system. hope this helps... -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Jul 18 12:51:49 2002 Received: from mail.csusb.edu ([139.182.2.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IGpnr02210 for ; Thu, 18 Jul 2002 12:51:49 -0400 Received: from mail.csusb.edu (localhost [127.0.0.1]) by mail.csusb.edu (8.12.5/8.12.5) with ESMTP id g6IGoB5j024516; Thu, 18 Jul 2002 09:50:11 -0700 (PDT) Received: from localhost (kcousins@localhost) by mail.csusb.edu (8.12.5/8.12.5/Submit) with SMTP id g6IGoAQc024507; Thu, 18 Jul 2002 09:50:11 -0700 (PDT) Date: Thu, 18 Jul 2002 09:50:10 -0700 (PDT) From: Kimberley Cousins To: SCT cc: chemistry@ccl.net Subject: babel for mac In-Reply-To: <3D3673CE.4B93F0EF@kcl.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone been able to get Babel for mac to work on a G3/G4 with System 9.x? I used to use this a while back, but now just get errors with either the with or without fpu code (won't execute). I'm using the only versions I can find; macbabel 1.3. Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins From chemistry-request@server.ccl.net Thu Jul 18 12:39:26 2002 Received: from web13405.mail.yahoo.com ([216.136.175.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6IGdPr01928 for ; Thu, 18 Jul 2002 12:39:25 -0400 Message-ID: <20020718163921.58077.qmail@web13405.mail.yahoo.com> Received: from [128.115.13.33] by web13405.mail.yahoo.com via HTTP; Thu, 18 Jul 2002 09:39:21 PDT Date: Thu, 18 Jul 2002 09:39:21 -0700 (PDT) From: eric hu Subject: Re: CCL:cartesian to pdb To: eric hu , chemistry@ccl.net Cc: pdb-l@rcsb.org In-Reply-To: <20020717171204.48795.qmail@web13405.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Of course I tried Babel first which I thought is the standard way to do this kind of thing. However babel can not assign the correct residue name according the cartesian coordinates (with the atom types). Eric --- eric hu wrote: > Hi, I wonder if there is an easy way to change the > cartesian coordinates to pdb format. Thanks! > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.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 > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com From chemistry-request@server.ccl.net Thu Jul 18 13:40:39 2002 Received: from mustang.mpi.com ([199.93.193.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IHedr03408 for ; Thu, 18 Jul 2002 13:40:39 -0400 Received: from lightning.mpi.com (lightning.mpi.com [199.93.192.53]) by mustang.mpi.com (Switch-2.2.2/Switch-2.2.0) with ESMTP id g6IHedX23231; Thu, 18 Jul 2002 13:40:39 -0400 (EDT) Received: from US-VS1.corp.mpi.com (us-be2.corp.mpi.com [199.93.195.21]) by lightning.mpi.com (Switch-2.2.2/Switch-2.2.0) with ESMTP id g6IHecZ21652; Thu, 18 Jul 2002 13:40:38 -0400 (EDT) X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Subject: RE: A Perplexing AIM question Date: Thu, 18 Jul 2002 13:39:47 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: A Perplexing AIM question Thread-Index: AcIueRcvW9qUGRO3SHGjst0/00oI8AACIudQ From: "Stradella, Omar" To: "Gary Breton" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6IHedr03409 > >Hello all, > >As there has been a rash of AIM questions as of late, I'd like to add one >more. > >If I take ethane and run a minimization of the structure at the >RB3LYP/6-31G(d) level I obtain a perfectly nice structure as expected. I >can take the Cartesian coordinates from the Gaussian output and create an >XYZ file that can be read within several programs, including the free >ViewerLite from Accelrys. All looks good, and I measure very reasonable C-C >bond lengths of 1.53 A, C-H bond of 1.10 and a C-C-H angle of 111.4 (and I >say all this just to prove I can create an XYZ file properly!). > >I then performed an AIM analysis on this structure within G98W (keywords: >output=wfn punch=archive aim). Furthermore, I then took the wavefunction >generated and subjected it to a calculation of its critical points in the >(formerly free) program AIM2000. > >Both G98W and AIM2000 generated exactly the same Cartesian coordinates for >the "attractors" and for the critical points on the attractor interaction >lines. (ok: so I can perform an AIM calculation properly, too!) > >Finally, I simply lifted the cartesian coordinates from either of these two >output files and created a new XYZ file (I use ghost atoms (Bq) to define >the critical points). When I view the structure though, the C-C bond is now >2.89 A (!!) and the C-H bond 2.04 A but the C-C-H bond angle remains the >same. (the same holds true if the Bq atoms are not included in the file). > Since: 2.89*0.529 = 1.53 and 2.04*0.529 = 1.08 and the angle is the same, that strongly suggests that 2.89 and 2.04 are distances in atomic units, not Angstrom. Omar >As the "attractors" are expected to simply be the atomic nuclei, why are >the >bond distances different from the minimized structure? The answer is not >obvious to me. > >Gary W. Breton >Chair and Associate Professor >Department of Chemistry >Berry College >PO Box 495016 >Mount Berry, GA 30149 > >"There's a light at the >end of the tunnel, but it >may be an oncoming train" > > > >-= 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 Wed Jul 17 08:53:53 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HCrrv21555 for ; Wed, 17 Jul 2002 08:53:53 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA17977; Wed, 17 Jul 2002 08:53:52 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 17 Jul 2002 08:52:12 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GZE0047V8VI7H@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Wed, 17 Jul 2002 08:47:42 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id <3VB0MB2Z>; Wed, 17 Jul 2002 08:50:59 -0400 Content-return: allowed Date: Wed, 17 Jul 2002 08:50:52 -0400 From: "Shobe, Dave" Subject: gapt charges To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15E97@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6HCrrv21556 Is there a program that, given a Gaussian freq checkpoint file, will compute GAPT charges and the d(dipole)/d(atom.xyz) tensors? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. From chemistry-request@server.ccl.net Thu Jul 18 16:06:28 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6IK6Sr07329 for ; Thu, 18 Jul 2002 16:06:28 -0400 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g6IK6NY01362; Thu, 18 Jul 2002 13:06:24 -0700 (PDT) Message-Id: <200207182006.g6IK6NY01362@mx.seanet.com> To: Gary Breton , From: Mark Thompson Subject: Re: CCL:A Perplexing AIM question Date: Thu, 18 Jul 2002 13:06:28 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 Dear Gary, Your unexpected bond distances look suspiciously like they are given in bohrs and not angstroms (2.89 * 0.529177 = 1.53) I'll bet the outputs are generated in atomic units. Mark ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= > Hello all, > > As there has been a rash of AIM questions as of late, I'd like to add one > more. > > If I take ethane and run a minimization of the structure at the > RB3LYP/6-31G(d) level I obtain a perfectly nice structure as expected. I > can take the Cartesian coordinates from the Gaussian output and create an > XYZ file that can be read within several programs, including the free > ViewerLite from Accelrys. All looks good, and I measure very reasonable C-C > bond lengths of 1.53 A, C-H bond of 1.10 and a C-C-H angle of 111.4 (and I > say all this just to prove I can create an XYZ file properly!). > > I then performed an AIM analysis on this structure within G98W (keywords: > output=wfn punch=archive aim). Furthermore, I then took the wavefunction > generated and subjected it to a calculation of its critical points in the > (formerly free) program AIM2000. > > Both G98W and AIM2000 generated exactly the same Cartesian coordinates for > the "attractors" and for the critical points on the attractor interaction > lines. (ok: so I can perform an AIM calculation properly, too!) > > Finally, I simply lifted the cartesian coordinates from either of these two > output files and created a new XYZ file (I use ghost atoms (Bq) to define > the critical points). When I view the structure though, the C-C bond is now > 2.89 A (!!) and the C-H bond 2.04 A but the C-C-H bond angle remains the > same. (the same holds true if the Bq atoms are not included in the file). > > As the "attractors" are expected to simply be the atomic nuclei, why are the > bond distances different from the minimized structure? The answer is not > obvious to me. > > Gary W. Breton > Chair and Associate Professor > Department of Chemistry > Berry College > PO Box 495016 > Mount Berry, GA 30149 > > "There's a light at the > end of the tunnel, but it > may be an oncoming train" > > > > -= 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 > > > > > > ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Thu Jul 18 19:42:47 2002 Received: from mtiwmhc21.worldnet.att.net ([204.127.131.46]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6INglr17316 for ; Thu, 18 Jul 2002 19:42:47 -0400 Received: from dopetec ([138.23.156.82]) by mtiwmhc21.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020718234242.EGXT17970.mtiwmhc21.worldnet.att.net@dopetec> for ; Thu, 18 Jul 2002 23:42:42 +0000 Message-ID: <007601c22eb4$cf5b3fd0$529c178a@dopetec> From: "Donald Keidel" To: Subject: does Gaussian98 run well on supercomputers Date: Thu, 18 Jul 2002 16:42:40 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0073_01C22E7A.21E57990" 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_0073_01C22E7A.21E57990 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I am considering applying for an allocation of time on one of the NPACI = supercomputerrs to run Gaussian 98 calculations. I am wondering thought = if Gaussian98 was written to run nicely in parallel on thesee machines = or is it just as good on a single processor machine? Thank you to = everyone. Don Keidel -------------------------------------------------------------------------= -------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0073_01C22E7A.21E57990 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
 
I am considering applying for an = allocation of time=20 on one of the NPACI supercomputerrs to run Gaussian 98 = calculations.  I am=20 wondering thought if Gaussian98 was written to run nicely in parallel on = thesee=20 machines or is it just as good on a single processor machine?  = Thank you to=20 everyone.
 
Don Keidel
 
 
----------------------------------------------------------------= -----------------------------------------------
Donald=20 J. Keidel
University of California, Riverside
Department of = Biochemistry=20 and Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /FONT>
 
 
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