From chemistry-request@server.ccl.net Wed Aug 9 03:09:48 2000 Received: from balder.nilu.no (balder.nilu.no [128.39.104.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA02988 for ; Wed, 9 Aug 2000 03:09:47 -0400 Received: from afrodite.no. (afrodite.nilu.no) by balder.nilu.no (Sun Internet Mail Server sims.3.5.2000.01.05.12.18.p9) with ESMTP id <0FZ000J9EJW2TG@balder.nilu.no> for chemistry@ccl.net; Wed, 9 Aug 2000 09:09:39 +0200 (MET DST) Received: from eshpc (eshpc.nilu.no. [128.39.66.15]) by afrodite.no. (8.9.1b+Sun/8.9.1) with SMTP id JAA11352 for ; Wed, 09 Aug 2000 09:09:34 +0200 (MET DST) Date: Wed, 09 Aug 2000 09:09:28 +0200 From: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Subject: Autodock: Atomic charges in protein pdbq format To: CCL Reply-to: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Message-id: <003901c001d0$c24067c0$0f422780@nilu.no> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Priority: 3 Autodock users, As new users in Autodock we are looking for alternatives to the software package Sybyl to add polar H and Kollman united-atom partial atomic charges (columns 71-76 in pdbq format). Does any of you use the program 'prepare' (incl. 'protonate', 'q-kollua') to do this ? Thanks in advance, ######################################### Eldbjørg S. Heimstad NILU Norwegian Institute for Air Research The Polar Environmental Centre N-9296 Tromsø, Norway Tel. +47-77 75 03 75 Fax. +47-77 75 03 76 E-mail: Eldbjorg.Sofie.Heimstad@nilu.no Web: http://www.nilu.no ######################################### From chemistry-request@server.ccl.net Wed Aug 9 04:15:06 2000 Received: from atc.atccu.chula.ac.th (un@atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03514 for ; Wed, 9 Aug 2000 04:14:46 -0400 Received: from localhost (un@localhost) by atc.atccu.chula.ac.th (8.9.1/8.9.1) with ESMTP id PAA02184 for ; Wed, 9 Aug 2000 15:32:02 +0700 Date: Wed, 9 Aug 2000 15:32:02 +0700 (ICT) From: chinapong kritayakornupong To: chemistry@ccl.net Subject: convert x-ray data to cartesian coordinate Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have the x-ray data which in the latic coordinate. I would like to know which program that can convert the latic coordinate (x-ray data) to the cartesian coordinate? looking forword to hear from you. Thank you, Chinapong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Chinapong Kritayakornupong %% %% M.Sc. student %% %% Department of Chemistry %% %% Faculty of Science %% %% Chulalongkorn University %% %% Thailand 10330 %% %% Office Room (66)(2)2185221-2 %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@server.ccl.net Wed Aug 9 05:11:25 2000 Received: from lozen.uit.no (lozen.Uit.No [129.242.5.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA03722 for ; Wed, 9 Aug 2000 05:11:25 -0400 Received: from james.chem.uit.no (james.Chem.Uit.No [129.242.24.111]) by lozen.uit.no (8.10.1/8.10.1) with ESMTP id e799BG502046 for ; Wed, 9 Aug 2000 11:11:16 +0200 (METDST) Received: from chem.uit.no (uran.Chem.Uit.No [129.242.24.167]) by james.chem.uit.no (8.9.3/8.9.3) with ESMTP id LAA74398 for ; Wed, 9 Aug 2000 11:16:05 +0200 (CEST) Sender: tsaue@chem.uit.no Message-ID: <39912033.6E1A2C2C@chem.uit.no> Date: Wed, 09 Aug 2000 11:11:15 +0200 From: Trond Saue X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: CCL: Time-dependent Schroedinger equation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit What non-trivial (that is non-stationary) exact solutions of the time-dependent Schroedinger equation for a given model system are known ? All the best, Trond Saue -- ********************************************************************** * Trond Saue * Universitetet i Tromsoe Phone: +47/77645205 * Institutt for kjemi, MNF Fax : +47/77644765 * N-9037 TROMSOE, NORWAY * Check out the DIRAC home page: * http://dirac.chem.sdu.dk/ * WEB: http://www.chem.uit.no/KJEMI/TEOCHEM/trond.html * *********************************************************************** From chemistry-request@server.ccl.net Wed Aug 9 09:38:42 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA05679 for ; Wed, 9 Aug 2000 09:38:42 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id JAA17567; Wed, 9 Aug 2000 09:38:14 -0400 (EDT) Date: Wed, 9 Aug 2000 09:38:14 -0400 (EDT) From: "C.F. Matta" To: chinapong kritayakornupong cc: chemistry@ccl.net Subject: Re: CCL:convert x-ray data to cartesian coordinate In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Chinapong, I use a program called Mol2Mol (Ver. 3.21)that does exaclty that. You input the cell parameters and the fractional coordinates and you will get cartesian coordinates, and if you want you can get a z-matrix (and many other outputs). I find it extremely useful. Mol2Mol runs under a Windows platform. It is downloadable at: http//www.compuchem.com Take care. Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University _______________________ Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ On Wed, 9 Aug 2000, chinapong kritayakornupong wrote: > Dear all, > I have the x-ray data which in the latic coordinate. I would like > to know which program that can convert the latic coordinate (x-ray > data) to the cartesian coordinate? > looking forword to hear from you. > Thank you, > Chinapong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% Chinapong Kritayakornupong %% > %% M.Sc. student %% > %% Department of Chemistry %% > %% Faculty of Science %% > %% Chulalongkorn University %% > %% Thailand 10330 %% > %% Office Room (66)(2)2185221-2 %% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > -= 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 Wed Aug 9 11:41:18 2000 Received: from mailer.syr.edu (mailer.syr.edu [128.230.18.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06191 for ; Wed, 9 Aug 2000 11:41:18 -0400 Received: from gamera.syr.edu by mailer.syr.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.00513B2F@mailer.syr.edu>; Wed, 9 Aug 2000 11:41:05 -0400 Received: from localhost (ctmiddle@localhost) by gamera.syr.edu (8.8.7/8.8.7) with ESMTP id LAA29253; Wed, 9 Aug 2000 11:41:05 -0400 (EDT) X-Authentication-Warning: gamera.syr.edu: ctmiddle owned process doing -bs Date: Wed, 9 Aug 2000 11:41:05 -0400 (EDT) From: "Chris T. Middleton" X-Sender: ctmiddle@gamera.syr.edu To: chemistry@ccl.net cc: ochtersk@gaussian.com Subject: Z Matrix for [2.2]Paracyclophane Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am trying to create a Z Matrix for [2.2]Paracyclophane (two benzene rings connected by two ethano bridges at the para positions). I have tried a couple different ways of forming the matrix but have been able to get Gaussian98 to recognize the D2 symmetry. It is a complex problem due to the molecules low symmetry and large size. At "http://hudsonlab.syr.edu/paracyclophane.html" I have placed a picture of the molecule along with the last Z Matrix I attempted. If anyone can see where I went wrong in the Z Matrix, I would greatly appreciate any information. I have also considered the possiblity that I am mistaken as to how Gaussian recognizes the symmetry in Z Matrices. Any information about this wuold also be very helpfull. Thank you, Chris Middleton Syracuse University From chemistry-request@server.ccl.net Wed Aug 9 14:58:30 2000 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07081 for ; Wed, 9 Aug 2000 14:58:29 -0400 Received: (from sharmay@localhost) by helix.nih.gov (8.9.3/8.9.3) id OAA646566; Wed, 9 Aug 2000 14:58:30 -0400 (EDT) Date: Wed, 9 Aug 2000 14:58:30 -0400 From: Yugal Sharma To: chemistry@ccl.net Subject: G98 shielding calculation using isotopes? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am currently running Gaussian 98 (SGI-G98RevA.6) to calculate NMR shielding tensors for various residues in a protein. I was wondering if anyone knew of a way to incorporate different isotopes into the calculations (e.g. calculating the shielding for 15N versus the default for 14N)? Thanks much. Best regards, Yugal ***************************************************************** Yugal Sharma Tel: (301) 402-0617 National Institutes of Health Email: sharmay@helix.nih.gov Bethesda, MD USA ***************************************************************** From chemistry-request@server.ccl.net Wed Aug 9 15:23:56 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA07204 for ; Wed, 9 Aug 2000 15:23:56 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id PAA23396 for ; Wed, 9 Aug 2000 15:23:56 -0400 (EDT) Message-ID: <012101c00237$c23369a0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "CCL - all" Subject: Fw: writing symmetric Z-matrices - was CCL: Z Matrix for [2.2]Paracyclophane Date: Wed, 9 Aug 2000 15:26:46 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Chris, there are two possible sources to your problem: * your z-matrix may not be symmetric * the program may be unable to recognize the symmetry of the molecule I guess that Gaussian analyzes symmetry in cartesian coordinates. I am convinced that the format of your geometry specification (z-matrix, cartesians, ...) is immaterial. Without looking at the values of your variables I can't say if your molecule is symmetric. It may be C1, since you have more variables than internal degrees of freedom. The reasoning is as follows: In D2 symmetry your molecule has 8 symmetry unique atoms, e.g. 1,2,3,4,17,18,19,20. You need 8*3-6=18 variables to specify that geometry. The relation to the copy with 9,10,11,12 needs three variables (RR,RRG and GRRG) and defines the horizontal C2 axis. Only two more variables are needed to fix the remaining 16 atoms in space: the distance between the centers of the 4-9 and 8-13 bonds confines the remaining two C2 axis into a plane and the torsion angle 4-(4-9)-(8-13)-8 fixes those two C2 axes. You use 6 variables to glue these two groups together. In other words, your z-matrix is overdetermined and only certain combinations of OG, OGY, GOY, OGYO,YOGY and GYOG are D2 symmetric. A Z-matrix that enforces D2 symmetry could look like this: X X 1,r2 C 1,r3 2,90. C 3,r4 1,a4 2,d4 C 4,r5 3,a5 1,d5 C 5,r6 4,a6 3,d6 C 1,r3 2,90. 3,180. C 7,r4 1,a4 2,d4 C 8,r5 7,a5 1,d5 C 9,r6 8,a6 7,d6 C 2,r3 1,90. 3,d11 C 11,r4 2,a4 1,d4 C 12,r5 11,a5 2,d5 C 13,r6 12,a6 11,d6 C 2,r3 1,90. 11,180. C 15,r4 2,a4 1,d4 C 16,r5 15,a5 2,d5 C 17,r6 16,a6 15,d6 ... Since your molecule is somewhat spherical numerical inaccuracies may lead to a slight misplacement of the principal axes which results in recognizing a lower symmetry, e.g.C2. I saw that once in a different program. Good luck, Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Aug 9 06:54:08 2000 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA05038 for ; Wed, 9 Aug 2000 06:54:07 -0400 Received: from pat.biochem.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 9 Aug 2000 11:53:12 +0100 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id LAA11031 for ; Wed, 9 Aug 2000 11:53:21 +0100 Date: Wed, 9 Aug 2000 11:53:20 +0100 (BST) From: Irilenia Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: P.S. to Summary of Software for Chemical Databases Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I apologise for not mentioning in my previous e-mail the Daylight software (Database Package etc) for creating and searching databases of chemical structures. As Daylight have provided us with SMILES, I ought to have put them in the list. I also received an e-mail from CambridgeSoft reminding me that they have a product that fits my description. It's called ChemFinder and it can interface to Oracle. Add it to the previous list (but you've got to be a Windows fan for this one I think :) ). Regards, Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk tel. 020 7679 2171 fax. 020 7679 7193 >>> The greatest proof of the existence of intelligent life outside Earth is that they haven't contacted us yet. <<<< From chemistry-request@server.ccl.net Wed Aug 9 10:46:07 2000 Received: from ans2.spri.sp.com (sp2.spcorp.com [198.16.9.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA05970 for ; Wed, 9 Aug 2000 10:46:07 -0400 Received: from kenmsgrly01.schp.com by sp2.spcorp.com with SMTP id KAA19998 (InterLock SMTP Gateway 4.2 for ); Wed, 9 Aug 2000 10:45:52 -0400 (EDT) Message-ID: <200008091445.KAA19998@sp2.spcorp.com> Received: FROM kenmsgbham03.schp.com BY kenmsgrly01.schp.com ; Wed Aug 09 10:45:51 2000 -0400 Received: by kenmsgbham03.schp.com with Internet Mail Service (5.5.2448.0) id ; Wed, 9 Aug 2000 10:45:51 -0400 From: "DUCA, JOSE" To: chemistry@ccl.net Subject: pKa computation Date: Wed, 9 Aug 2000 10:33:00 -0400 Importance: high X-Priority: 1 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) 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 KAA05971 Dear CCLers, I have a few questions on pKa calculation methods: 1. Is there any reliable method out there to compute pKa's for C-H systems? 2. How good is/can be the approach used in ACD Labs for C-H groups? 3. Any hints to use ab initio methods to obtain pKa's? Any help on this will be greatly appreciated. José Duca From chemistry-request@server.ccl.net Wed Aug 9 11:58:01 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06284 for ; Wed, 9 Aug 2000 11:58:00 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA19904 for ; Wed, 9 Aug 2000 08:53:46 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost.msi.com via smap (V2.0) id xma019902; Wed, 9 Aug 00 08:53:22 -0700 Message-Id: <4.3.2.7.0.20000809084317.00af8cd0@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 09 Aug 2000 08:46:48 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Customer Training in North Carolina Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of workshops focusing on InsightII at the North Carolina Supercomputing Center, Research Triangle Park, NC. Space is limited in these workshops so sign up early. On October 3-4, the workshop "Life Science Modeling in InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On October 5-6, the "Homology Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from a primary amino acid sequence will be covered step-by-step. Prerequisites for this course are the "Life Science Modeling in InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for the both courses and receive a 25% discount for the second workshop. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Beverly Batchelder 858-799-5711 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Wed Aug 9 17:42:00 2000 Received: from sg1503.chemie.uni-marburg.de (giju@sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA08513 for ; Wed, 9 Aug 2000 17:42:00 -0400 Received: from localhost (giju@localhost) by sg1503.chemie.uni-marburg.de (8.11.0/8.11.0/schn) with ESMTP id e79LfwZ09140; Wed, 9 Aug 2000 23:41:58 +0200 (MEST) Date: Wed, 9 Aug 2000 23:41:57 +0200 From: Kalathingal Thomas Giju To: CHEMISTRY@ccl.net cc: CCL - all Subject: Re: CCL:Fw: writing symmetric Z-matrices - was Z Matrix for [2.2]Paracyclophane In-Reply-To: <012101c00237$c23369a0$bbc0e380@qtp.ufl.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Everybody, On Wed, 9 Aug 2000, Stefan Fau wrote: > Hi Chris, > > there are two possible sources to your problem: > * your z-matrix may not be symmetric > * the program may be unable to recognize the > symmetry of the molecule > > I guess that Gaussian analyzes symmetry in > cartesian coordinates. I am convinced that the > format of your geometry specification (z-matrix, > cartesians, ...) is immaterial. > > Without looking at the values of your variables > I can't say if your molecule is symmetric. It may > be C1, since you have more variables than > internal degrees of freedom. > > The reasoning is as follows: > In D2 symmetry your molecule has 8 symmetry > unique atoms, e.g. 1,2,3,4,17,18,19,20. You > need 8*3-6=18 variables to specify that geometry. > The relation to the copy with 9,10,11,12 needs > three variables (RR,RRG and GRRG) and defines > the horizontal C2 axis. Only two more variables are > needed to fix the remaining 16 atoms in space: the > distance between the centers of the 4-9 and 8-13 > bonds confines the remaining two C2 axis into a plane > and the torsion angle 4-(4-9)-(8-13)-8 fixes those > two C2 axes. You use 6 variables to glue these two > groups together. In other words, your z-matrix is > overdetermined and only certain combinations of > OG, OGY, GOY, OGYO,YOGY and GYOG > are D2 symmetric. I am not an expert on the Z-matrix. However, when I had run the same molecule I needed 24 variables to enforce D2 symmetry. Not "8*3-6=18"!!!!!!!!! Am I right? Stoichiometry C16H16 Framework group D2[X(C16H16)] Deg. of freedom 24 Full point group D2 NOp 4 Largest Abelian subgroup D2 NOp 4 Largest concise Abelian subgroup D2 NOp 4 --------------------------------------------------- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* * Dr. Kalathingal T. Giju * * Humboldt Research Fellow * * Fachbereich Chemie, Universitaet Marburg * * Hans-Meerwein-Strasse * * D-35032 Marburg/Lahn, Germany. * * e-mail: gijukt@mailer.uni-marburg.de * * URL: http://staff-www.uni-marburg.de/~kalathin * * Telephone: 0049-6421-2826523 * * Fax : 0049-6421-2828917 * *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* --------------------------------------------------- From chemistry-request@server.ccl.net Wed Aug 9 19:06:44 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA08918 for ; Wed, 9 Aug 2000 19:06:44 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id TAA25027; Wed, 9 Aug 2000 19:06:38 -0400 (EDT) Message-ID: <013f01c00256$de9f78d0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Kalathingal Thomas Giju" Cc: "CCL - all" Subject: Re: CCL: writing symmetric Z-matrices - was Z Matrix for[2.2]Paracyclophane Date: Wed, 9 Aug 2000 19:09:28 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Kalathingal, thanks for pointing out my error. Indeed there are 24 internal degrees of freedom. 18 are needed to fix the geometry of the symmetry unique C4H4 fragment. 3 fix the position of one atom in the first image and one more (which I overlooked in the previous message) is needed for the dihedral angle across the bond connecting original and image. The last two degrees of freedom describe the distance between this and the other 16 atom unit and the associated dihedral angle. 18+3+1+1+1=24. Stefan ----- Original Message ----- From: Kalathingal Thomas Giju To: Cc: CCL - all Sent: Wednesday, August 09, 2000 5:41 PM Subject: CCL:Fw: writing symmetric Z-matrices - was Z Matrix for[2.2]Paracyclophane > > Hi Everybody, > > On Wed, 9 Aug 2000, Stefan Fau wrote: > > > Hi Chris, > > > > there are two possible sources to your problem: > > * your z-matrix may not be symmetric > > * the program may be unable to recognize the > > symmetry of the molecule > > > > I guess that Gaussian analyzes symmetry in > > cartesian coordinates. I am convinced that the > > format of your geometry specification (z-matrix, > > cartesians, ...) is immaterial. > > > > Without looking at the values of your variables > > I can't say if your molecule is symmetric. It may > > be C1, since you have more variables than > > internal degrees of freedom. > > > > The reasoning is as follows: > > In D2 symmetry your molecule has 8 symmetry > > unique atoms, e.g. 1,2,3,4,17,18,19,20. You > > need 8*3-6=18 variables to specify that geometry. > > The relation to the copy with 9,10,11,12 needs > > three variables (RR,RRG and GRRG) and defines > > the horizontal C2 axis. Only two more variables are > > needed to fix the remaining 16 atoms in space: the > > distance between the centers of the 4-9 and 8-13 > > bonds confines the remaining two C2 axis into a plane > > and the torsion angle 4-(4-9)-(8-13)-8 fixes those > > two C2 axes. You use 6 variables to glue these two > > groups together. In other words, your z-matrix is > > overdetermined and only certain combinations of > > OG, OGY, GOY, OGYO,YOGY and GYOG > > are D2 symmetric. > > I am not an expert on the Z-matrix. However, when I had > run the same molecule I needed 24 variables to enforce > D2 symmetry. Not "8*3-6=18"!!!!!!!!! > Am I right? > > Stoichiometry C16H16 > Framework group D2[X(C16H16)] > Deg. of freedom 24 > Full point group D2 NOp 4 > Largest Abelian subgroup D2 NOp 4 > Largest concise Abelian subgroup D2 NOp 4 > > > --------------------------------------------------- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > * Dr. Kalathingal T. Giju * > * Humboldt Research Fellow * > * Fachbereich Chemie, Universitaet Marburg * > * Hans-Meerwein-Strasse * > * D-35032 Marburg/Lahn, Germany. * > * e-mail: gijukt@mailer.uni-marburg.de * > * URL: http://staff-www.uni-marburg.de/~kalathin * > * Telephone: 0049-6421-2826523 * > * Fax : 0049-6421-2828917 * > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > --------------------------------------------------- > > > > > -= 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 > > ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Aug 9 20:46:04 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA09461 for ; Wed, 9 Aug 2000 20:46:04 -0400 Received: from localhost (mdb@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id RAA19456 for ; Wed, 9 Aug 2000 17:45:59 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: mdb owned process doing -bs Date: Wed, 9 Aug 2000 17:45:59 -0700 (PDT) From: "Michael D. Bartberger" Reply-To: "Michael D. Bartberger" To: Computational Chemistry List Subject: AutoDock 3.0 Compilation on Linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all: I am having a problem with AutoDock under Red Hat Linux 6.2. (2.2.16-3smp kernel, although I am, of course, only trying to compile AutoDock in serial for use on 1 processor). Using the source code from ver. 3.00, and the instructions of Pierre Scotney for patching AutoDock 3.0 located at http://www.medstv.unimelb.edu.au/~pierre/autodock/ I was able to compile each of the modules (autotors, autogrid, autodock) with no problem. Using a sample input from a project of one of our students (which runs succesfully on an SGI) I tested out the Linux port. Autotors runs perfectly and gives correct reults. However, I am having a problem with autodock. The program seems to run; however, there appears to be what looks like a serious memory leak or garbage collection problem (pardon my ignorance; I'm not quite sure). What happens is that memory usage for the job, as indicated by 'top' (our boxes are equipped with 512 MB of RAM) climbs higher and higher, past the point where all physical memory is exceeded and the program begins encroaching on swap space. The machine then slows to a crawl as the swap partition thrashes. Even the swap use climbs higher and higher (with all physical memory being used by the program as well) until the job is killed by hand. Something is definitely wrong. Our nodes are dual Pentium-III 800 MHz machines with an out-of-the-box installation of Red Hat Linux 6.2, which has been upgraded to the 2.2.16-3smp kernel as provided by Red Hat in RPM form. We are simply trying to run autodock in serial on one of the processors in this box. All compilers, libraries, etc. are directly from the RH 6.2 CD. There is nothing particularly exotic about our OS/software installation. I was curious if anyone has seen such behavior before, and if so, whether a workaround might exist. Alternatively, a new/different set of compilation instructions/patches starting with "fresh" AutoDock 3.0 source would also be appreciated. I notice that Scripps has an AutoDock version 3.05 now, and perhaps that might be worth a try. Thanks in advance for any assistance anyone can provide. Best regards, -Mike Bartberger Chemistry/Biochemistry, UCLA +-----------------------------------------------------------------+ | Michael D. Bartberger, Ph.D. TEL: 310.206.0553 | | Department of Chemistry and Biochemistry FAX: 310.206.1843 | | University of California, Los Angeles | | Los Angeles, California 90095-1569 mdb@chem.ucla.edu | +-----------------------------------------------------------------+