From chemistry-request@server.ccl.net Wed Aug 29 00:37:22 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7T4bLM18803 for ; Wed, 29 Aug 2001 00:37:21 -0400 Received: from ISOSIRRI (dhcp-28.csc.fi [193.166.2.28]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id HAA28115; Wed, 29 Aug 2001 07:37:19 +0300 From: "Leif Laaksonen" To: "'Sergio Manzetti'" , "'Chemistry Discussion G'" Subject: RE: GROMACS simulation trajectories Date: Wed, 29 Aug 2001 07:37:13 +0300 Message-ID: <000001c13044$46f00910$1c02a6c1@ISOSIRRI> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: Hi, gOpenMol can work with the GROMACS trajectories. http://www.csc.fi/~laaksone/gopenmol/ Regards, -leif laaksonen -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Sergio Manzetti Sent: Wednesday, August 29, 2001 8:50 AM To: Chemistry Discussion G Subject: CCL:GROMACS simulation trajectories Hi all, I would like to know if anyone knows about any programs that can work with the trajectories outputted from GROMACS, and visualize and maybe even export them to AVS file formats. Cheers Sergio ________________________________________________________________________ ____ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ -= 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 29 01:18:09 2001 Received: from mumbai3.mtnl.net.in ([203.94.227.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7T5I4M20148 for ; Wed, 29 Aug 2001 01:18:05 -0400 Received: from bol.net.in by mumbai3.mtnl.net.in (8.9.1/1.1.20.3/10Aug01-0930PM) id KAA0000023950; Wed, 29 Aug 2001 10:46:45 +0530 (IST) Message-ID: <3B8C7EAF.482F90BF@bol.net.in> Date: Wed, 29 Aug 2001 11:03:36 +0530 From: Prashant Desai X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Posting Question on CCL Subject: Bootstrap Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking out for information about theory and application of Bootstrap algorithm as applied for vaidation of QSAR equations. Any relevant refrences and reprints are welcome. Prashant Desai Senior Research Fellow Dept. Pharm. Chem. Bombay College of Pharmacy University of Mumbai Mumbai, IndiA. From chemistry-request@server.ccl.net Wed Aug 29 05:51:40 2001 Received: from c0mailgw07.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7T9paM12424 for ; Wed, 29 Aug 2001 05:51:39 -0400 Received: from c0web105 (216.163.180.10) by c0mailgw07.prontomail.com (NPlex 5.5.029) id 3B7C488D002D5031 for chemistry@ccl.net; Wed, 29 Aug 2001 02:44:15 -0700 From: "markus mayer" Message-Id: <4210F72F75C95D115A550005B88C07F2@mayer.nandomail.com> Date: Wed, 29 Aug 2001 02:44:15 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: simulated annealing optimimum structure X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear all, I want to determine the ground state of a crystal structure only very few is know about the geometry of the unit cell. Somebody suggested that I should try to use simulated annealing in doing this. Since I only did a few MD calculation in my life, would you please verify whether the below is true in the procedure? 1. I can use the minimum unit cell (instead of very big cell when studying melting) 2. I raise the temperature to 1000 K, let it run for several hundred time steps (time step several fs or so). 3. Sample the configuration at the last steps to determine how coordinates become. 4. Lower the temperature, run it again, is 50K a good temperature step? Hopefully at last I would get the zero temperature ground state I want??? thanks very much in advance for your help markus ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Wed Aug 29 10:33:55 2001 Received: from hotmail.com ([216.33.149.70]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TEXtM19091 for ; Wed, 29 Aug 2001 10:33:55 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 29 Aug 2001 07:33:49 -0700 Received: from 147.29.185.130 by lw4fd.law4.hotmail.msn.com with HTTP; Wed, 29 Aug 2001 14:33:49 GMT X-Originating-IP: [147.29.185.130] From: "rah rach" To: chemistry@ccl.net Subject: Phthalates, Data? Date: Wed, 29 Aug 2001 16:33:49 +0200 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 29 Aug 2001 14:33:49.0518 (UTC) FILETIME=[9E2F4EE0:01C13097]
Hi every one ,
 
I am looking for data( physical properties data , as normal boiling point , vapour pressure ,....) for the phthalates compounds . If any one can helpe me by indicating any source ( programs, databook, articles,...etc) I would appreciate that very much .
thanks in advance.
R.Rachid

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From chemistry-request@server.ccl.net Wed Aug 29 09:56:44 2001 Received: from hotmail.com ([216.32.181.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TDuhM18618 for ; Wed, 29 Aug 2001 09:56:43 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 29 Aug 2001 06:56:38 -0700 Received: from 196.1.114.240 by lw2fd.hotmail.msn.com with HTTP; Wed, 29 Aug 2001 13:56:37 GMT X-Originating-IP: [196.1.114.240] From: "Kamalakar Jadhav" To: chemistry@ccl.net Subject: MSE_PROP 1.2 release Date: Wed, 29 Aug 2001 13:56:37 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 29 Aug 2001 13:56:38.0175 (UTC) FILETIME=[6C3362F0:01C13092] **** Announcement of release 1.2 of MSE_PROP **** MSE_PROP is a program for analysis of wavefunction (obtained from Gaussian 94/98,GAMESS or other ab-initio programs) that allows evalution of molecular properties (MESP, Electron density,etc) and visulization of the those properties. **** Features Added in New Release of MSE_PROP **** Evaluation and Visualization of Properties: · Electron Localization Function (ELF). · Average Ionization Potential / Energy and Molecular Orbitals. Geometries of intermolecular Complexes · Molecular Docking (vdW + Electrostatic) and EPIC Method. Special features Added · Computation of statistical parameters (average, variance, surface area etc.) for any property on vdW and user defined surface (e.g. 0.001 au electron density surface). · Facility to change atom properties and viewing vibrational frequencies. · Several new basis-sets added and labeling selected atoms in molecule. · Online Help, New user manual and tutorial. * MSE_PROP demo supports molecules up to Seven atoms and full version up to 150 atoms. System Requirements: Pentium x,Windows 95/98/NT,64 MB RAM,4 MB SVGA Card Interested? For more information and downloading the demo version, go to http://www.mahindrabt.com/services/cc_prod.htm _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Aug 29 08:54:54 2001 Received: from web14902.mail.yahoo.com ([216.136.225.54]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7TCssM17056 for ; Wed, 29 Aug 2001 08:54:54 -0400 Message-ID: <20010829125453.28146.qmail@web14902.mail.yahoo.com> Received: from [161.142.9.196] by web14902.mail.yahoo.com via HTTP; Wed, 29 Aug 2001 05:54:53 PDT Date: Wed, 29 Aug 2001 05:54:53 -0700 (PDT) From: Ng Pei Ling Subject: Hyperchem-Chemdraw To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii To all my dear friends: I'm doing project on "Calculating the binding energy of flavonoids with calcium by using computational methods for kidney stones research" Can somebody send me some journal that describe the method how to use hyperchem and chemdraw to compute by using the method of molecular mechanic, minimization energy, ab initio, monte carlo, molecular dynamics? I need the full text if possible. Thanks for your help. __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Wed Aug 29 12:10:34 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TGAXM21191 for ; Wed, 29 Aug 2001 12:10:33 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA24137; Wed, 29 Aug 2001 12:10:32 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B8D0E11.C6EC4648@cornell.edu> Date: Wed, 29 Aug 2001 11:45:21 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Phthalates, Data? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Hi every one , I am looking for data( physical properties data , as > normal boiling point , vapour pressure ,....) for the phthalates > compounds . If any one can helpe me by indicating any source ( > programs, databook, articles,...etc) I would appreciate that very much > .thanks in advance.R.Rachid > Hi > ----------------------------------------------------------------------- > Get your FREE download of MSN Explorer at http://explorer.msn.com > > -= 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 > > > Hi Try the CRC Handbook of Chemistry and Physics (or some similar reference), perhaps? Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Aug 29 14:03:36 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TI3WM23956 for ; Wed, 29 Aug 2001 14:03:36 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id NAA11004 for ; Wed, 29 Aug 2001 13:01:56 -0500 (CDT) Date: Wed, 29 Aug 2001 13:01:56 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: initial PDB file-bond distances Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, iam writing a small code (using AMBER parameters) for a protein. My question is the bond distances of the protein(from the PDB file) are different from the AMBER bond distances, and hence the bond potential energy is large(protein size: ~2500 atoms, bond energy ~ 30K kcal/mol) is this normal?i.e., the bond distances of the PDB file being so different from the AMBER parameter bond distances ?..is there anything i need to do with the bond distances of the PDB file before the MD code ? Thanks vani From chemistry-request@server.ccl.net Wed Aug 29 11:15:59 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TFFrM19941 for ; Wed, 29 Aug 2001 11:15:58 -0400 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Wed, 29 Aug 2001 16:14:16 +0100 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667D68@GABRIELLE> From: "Robinson, James" To: "'rah rach'" , chemistry@ccl.net Subject: RE: Phthalates, Data? Date: Wed, 29 Aug 2001 16:13:56 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" I often get data from Chemfinder.com or even the Aldrich Catalogue... -----Original Message----- From: rah rach [mailto:rahrach@hotmail.com] Sent: Wednesday, August 29, 2001 3:34 PM To: chemistry@ccl.net Subject: CCL:Phthalates, Data? Hi every one , I am looking for data( physical properties data , as normal boiling point , vapour pressure ,....) for the phthalates compounds . If any one can helpe me by indicating any source ( programs, databook, articles,...etc) I would appreciate that very much . thanks in advance. R.Rachid _____ Get your FREE download of MSN Explorer at http://explorer.msn.com -= 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 29 10:57:41 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7TEvfM19569 for ; Wed, 29 Aug 2001 10:57:41 -0400 Received: from wiracocha (wiracocha.ee.sc.edu [129.252.22.166]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id PY1YQTSL; Wed, 29 Aug 2001 10:55:11 -0400 Message-ID: <001401c130b3$fa10aa80$a616fc81@ee.sc.edu> From: "Hernan P Figueroa" To: , "Hannes Loeffler" References: <87ae0k82wz.fsf@pc1.eidolon.net> Subject: CCL:modifying (tuncating) basis sets? Date: Wed, 29 Aug 2001 10:56:44 -0700 Organization: University of South Carolina MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Hi, I am working with diffuse basis set too, for Gold, Copper and Silver. As Hannes, I would like to know if those basis set can be deleted safely or they need to be recalculated, because the software that I am using (CRYSTAL98) can not manage diffuse basis set. Please, could somebody tell me how to recalculate these basis set (LANL2DZ, SBKJC, Stuttgart ITC) in order to avoid diffuse gaussian function? I appreciate any information, thanks. Hernan Figueroa Department of Electrical Engineering University of South Carolina Phone: 803-777-0392 e-mail: figueroh@engr.sc.edu ----- Original Message ----- From: Hannes Loeffler To: chemistry@CCL.net Sent: Tuesday, August 28, 2001 11:17 AM Subject: CCL:modifying (truncating) basis sets? Hello, I want to use the LANL2DZ for Cu(2+). Now, this basis set contains some diffuse functions which should be unnecessary for a cation. Some publications mention such truncated basis sets and some people in our lab also used to truncate basis sets. Well, I'm a little bit suspicious about such modifications. Should such modifications be done, i.e. is it safe? When should a function be considered as diffuse? (LANL2DZ for instance has three uncontracted (1 x s, 2 x p) functions with exponents that "look" small.) What about truncations in contracted functions? Hannes. -= 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