From chemistry-request@server.ccl.net Tue Dec 12 07:47:53 2000 Received: from hotmail.com (f230.law8.hotmail.com [216.33.241.230]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA09997 for ; Tue, 12 Dec 2000 07:47:53 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 12 Dec 2000 04:45:42 -0800 Received: from 62.0.54.60 by lw8fd.law8.hotmail.msn.com with HTTP; Tue, 12 Dec 2000 12:45:42 GMT X-Originating-IP: [62.0.54.60] From: "Ilya Savotin" To: chemistry@ccl.net Subject: (Poly)Sulfides UV-VIS spectra calculation Date: Tue, 12 Dec 2000 15:45:42 +0300 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 12 Dec 2000 12:45:42.0856 (UTC) FILETIME=[706E3C80:01C06439] Hello ! I Recently started to use CAChe Worksystem ver. 3.22. Now I work on UV-VIS spectra producing for the following compounds class:dimethyl(poly)sulfides, methan(poly)thiols and inorganic sulfide in aqueous medium including for example H2S, HS-, S=, CH3)2S, (CH3)2S2, CH3SH etc.I have difficulty to calibrate and fit the program for that compounds in aqueous medium. It means that calculated spectra do not fit experimental ones at any UV-transition calculation method for water or gas phase. Does anybody worked with the same or similar compounds ? In such case does anybody knows how to suit existing methods or produce new ones for this compounds class ? Does anybody know at least another computational programs that are able to produce the same calculations ? Are they calibrated for my class of compounds ? The secondary little problem: what is the measurement unit of molar extinction coefficient in UV-VIS spectra graphs in CAChe 3.22 ? Is it the same unit that is used in this spectroscopy field ? With best regards, Anatoly Goifman The Hebrew University of Jerusalem e-mail: benhalof@walla.co.il _____________________________________________________________________________________ Get more from the Web. FREE MSN Explorer download : http://explorer.msn.com From chemistry-request@server.ccl.net Tue Dec 12 11:23:10 2000 Received: from adrik.bchs.uh.edu (Adrik.BCHS.UH.EDU [129.7.40.222]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA10809 for ; Tue, 12 Dec 2000 11:23:09 -0500 Received: from localhost (jhuang@localhost) by adrik.bchs.uh.edu (8.10.1/8.10.1) with ESMTP id eBCFPQx439651 for ; Tue, 12 Dec 2000 10:25:26 -0500 (CST) Date: Tue, 12 Dec 2000 10:25:25 -0500 From: Joe Huang To: chemistry@ccl.net Subject: A question about CHARMM and T3E! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Recently, we got CHARMM(c27b3) from Harvard and tried to compile it in Cray T3E at NPACI. I compiled a MPI version successfully with the lib and include files under the directory /opt/ctl/mpt/mpt in T3E. But when I tried to run the CHARMM program in parallel, it looked like it's always running in one CPU mode no matter how many computing nodes I assign to the program. Can somebody tell me what I should do for this problem? Thanks!!! Joe -- Below is the beginning part of the output file. ---------------------------------------------- USING PVM3 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 27b3 August 15, 2000 Copyright(c) 1984,1992 President and Fellows of Harvard College All Rights Reserved Current operating system: CRAY T3E Created on 6/11/ 0 at 15:16:40 by user: CRAYT3E Maximum number of ATOMS: 60120, and RESidues: 32000 Current HEAP size: 7000000, and STACK size: 900000 Will be using 1 processor (maximum is 1) .....etc. ---------------------------------------------- **************************************** Hung-Chung (Joe) Huang, M.T., M.Sc. Department of Biology and Biochemistry University of Houston, Houston, TX 77204 Tel: (713) 743-8389, Fax: (713) 743-8351 e-mail: HCHuang@uh.edu http://adrik.bchs.uh.edu/~jhuang **************************************** From chemistry-request@server.ccl.net Wed Dec 13 07:19:31 2000 Received: from matavnet.hu (mail.matavnet.hu [195.228.240.10]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA17644 for ; Wed, 13 Dec 2000 07:19:26 -0500 Received: (qmail 12684 invoked from network); 13 Dec 2000 13:19:05 +0100 Received: from line-106-213.dial.matav.net (HELO chemaxon.com) (145.236.106.213) by mail.matavnet.hu with SMTP; 13 Dec 2000 13:19:05 +0100 Message-ID: <3A37695D.7089BCF0@chemaxon.com> Date: Wed, 13 Dec 2000 13:19:41 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemweb@ic.ac.uk Subject: New releases: Marvin 2.6 and JChem 1.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Marvin Applets 2.6, Marvin JavaBeans 2.6 and JChem 1.5 have been released. These 100% Java tools are useful for building internet, intranet, distributed or standalone chemical applications. They can be tried/downloaded at http://www.chemaxon.com/products.html Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. JChem provides chemical database searching capabilities by integration into relational database engines supporting SQL. Marvin Applets are free for FREE web sites. The MarvinSketch and MarvinView applications are FREE for academic and home users. New features of Marvin: - Stereo SMILES/Molfile import/export - Improved 2D coordinate calculation (cleaning) from SMILES/2D/3D - Rgroups and Rgfiles - Scrolling and highlighting atoms in MarvinView - Drag & drop (in the Swing versions) - Command line viewer application in the Beans - Application for interconverting various chemical formats. - Workarounds for Netscape6 - etc ... 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Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T: +3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Wed Dec 13 13:53:37 2000 Received: from server.iq.ufrj.br (server.iq.ufrj.br [146.164.30.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19369 for ; Wed, 13 Dec 2000 13:53:34 -0500 Received: from agy (bhering@pxq77.iq.ufrj.br [146.164.6.77]) by server.iq.ufrj.br (8.9.3/8.9.3) with SMTP id PAA19095 for ; Wed, 13 Dec 2000 15:21:55 GMT From: Daniel Lopes Bhering To: chemistry@ccl.net Subject: PC cluster Date: Sat, 29 Jul 2000 20:02:04 -0400 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00072920404800.00816@agy> Content-Transfer-Encoding: 8bit Hi CCLers, I would like to known if anyone has a cluster of PC running gaussian94 in Linux? What is the best way to do it? Thanks in advance, Daniel L. Bhering From chemistry-request@server.ccl.net Wed Dec 13 17:10:47 2000 Received: from uucphost.mcs.net (Kitten2.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA20167 for ; Wed, 13 Dec 2000 17:10:46 -0500 Received: from becky (P42-Chi-Dial-4.pool.mcs.net [205.253.224.234]) by uucphost.mcs.net (8.11.1/8.11.1) with SMTP id eBDMAjR88875 for ; Wed, 13 Dec 2000 16:10:45 -0600 (CST) (envelope-from rone@mcs.net) Message-ID: <001901c06551$545c8600$eae0fdcd@becky> From: "Rebecca Rone" To: "ccl" Subject: Fw: CCL:A question about CHARMM and T3E! Date: Wed, 13 Dec 2000 16:08:33 -0600 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 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear Joe, I guess you missed seeing my previous message. I am repeating it below. I think the variable name for the multi-processor command may be INODE or something similar. To store the velocity on a per atom basis you can use the fourth parameter column of the PDB format files. Just look at the standard CHARMm test scripts to see how to use the fourth parameter. The scripts should also show you the variable names for the velocity component. This re-creates the kinetic energy of the system within error limits, but the vector component will be recomputed in the next run. This is not a major problem since all dynamics runs should be calculated until they converge on an ensemble of structures. The QUANTA manual also has an example of how to store the velocity components in the fourth parameter and then color on them to see the "hot spots". As I have written before, the fourth parameter column of the PDB file is normally used by crystallographers to store the B value. However, CHARMm allows you to do a variety of little tricks with it. Including storing the velocity on a per atom basis. Regards, Becky Dr. Rebecca Rone Rone Biotechnology Consulting www.mcs.net/~rone ----- Original Message ----- From: "Rebecca Rone" To: "Joe Huang" Sent: Tuesday, December 12, 2000 12:59 PM Subject: Re: CCL:A question about CHARMM and T3E! > Dear Joe, > > CHARMM has a variable to assign the number of nodes internally to the > program as well as externally to the OS of the computer. I don't remember > the name off hand, but you should have no trouble finding it in the > documentation. > > Regards, > > Becky > Dr. Rebecca Rone > Rone Biotechnology Consulting > ----- Original Message ----- > From: "Joe Huang" > To: > Sent: Tuesday, December 12, 2000 10:44 AM > Subject: CCL:A question about CHARMM and T3E! > > > > Dear CCLers, > > Recently, we got CHARMM(c27b3) from Harvard and tried to compile it in > > Cray T3E at NPACI. > > I compiled a MPI version successfully with the lib and include files under > > the directory /opt/ctl/mpt/mpt in T3E. > > But when I tried to run the CHARMM program in parallel, it looked like > > it's always running in one CPU mode no matter how many computing nodes I > > assign to the program. Can somebody tell me what I should do for this > > problem? Thanks!!! > > > > Joe > > -- > > > > **************************************** > > Hung-Chung (Joe) Huang, M.T., M.Sc. > > Department of Biology and Biochemistry > > University of Houston, Houston, TX 77204 > > Tel: (713) 743-8389, Fax: (713) 743-8351 > > e-mail: HCHuang@uh.edu > > http://adrik.bchs.uh.edu/~jhuang > > **************************************** > > > > > > -= 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 Dec 13 14:14:00 2000 Received: from pob.huji.ac.il (pob.huji.ac.il [132.64.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA19474 for ; Wed, 13 Dec 2000 14:13:59 -0500 Received: from pob.huji.ac.il (ovadia.fiz.huji.ac.il [132.64.85.40]) by pob.huji.ac.il (8.11.1/8.11.1) with ESMTP id eBDJE0H27035 for ; Wed, 13 Dec 2000 21:14:00 +0200 (IST) Message-ID: <3A37CA9F.D0D5957@pob.huji.ac.il> Date: Wed, 13 Dec 2000 21:14:39 +0200 From: Anatoly Goifman Reply-To: tantra@pob.huji.ac.il Organization: Hebrew University X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en,ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: (Poly)Sulfides UV-VIS spectra calculation (2) Content-Type: multipart/alternative; boundary="------------E15359ECEB2D061189D32A2A" --------------E15359ECEB2D061189D32A2A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello ! I had obviously breakdown on my e-mail server walla.co.il from which the following message "Sulfides and polysulfides UV-VIS spectra calculation" from e-mail benhalof@walla.co.il was send. I ask anyone to send the answer to this new e-mail tantra@pob.huji.ac.il Here is the source text once again. << Hellow ! Recently I started to use CAChe Worksystem ver. 3.22. Now I work on UV-VIS spectra producing for the following compounds class: dimethyl(poly)sulfides, methan(poly)thiols and inorganic sulfide in aqueous medium including for example H2S, HS-, S=, (CH3)2S, (CH3)2S2, CH3SH etc. I have difficulty to calibrate and fit the program for that compounds in aqueous medium. It means that calculated spectra do not fit experimental ones at any UV-transition calculation method for water or gas phase. Does anybody worked with the same or similar compounds ? In such case does anybody knows how to suit existing methods or produce new ones for this compounds class ? Does anybody know at least another computational programs that are able to produce the same calculations ? Are they calibrated for my class of compounds ? The secondary little problem: what is the mesurement unit of molar extinction coefficient in UV-VIS spectra graphs in CAChe 3.22 ? Is it the same unit that is used in this spectroscopy field ? >> With best regards, Anatoly Goifman The Hebrew University of Jerusalem Phone: 972-2-6586260 Fax: 972-2-65856155 E-mail: tantra@pob.huji.ac.il --------------E15359ECEB2D061189D32A2A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello ! I had obviously breakdown on my e-mail server walla.co.il >from which the following message
"Sulfides and polysulfides UV-VIS spectra calculation" >from e-mail benhalof@walla.co.il was send.
I ask anyone to send the answer to this new e-mail tantra@pob.huji.ac.il Here is the source text
once again.

<<
Hellow !
Recently I started to use CAChe Worksystem ver. 3.22. Now I work on UV-VIS spectra producing for the following compounds class: dimethyl(poly)sulfides, methan(poly)thiols and inorganic sulfide in aqueous medium  including for example H2S, HS-, S=, (CH3)2S, (CH3)2S2, CH3SH etc. I have difficulty to calibrate and fit the program for that compounds in aqueous medium. It means that calculated spectra do not fit experimental ones at any UV-transition calculation method for water or gas phase. Does anybody worked with the same or similar compounds ? In such case does anybody knows how to suit existing methods or produce new ones for this compounds class ? Does anybody know at least another computational programs that are able to produce the same calculations ? Are they calibrated for my class of compounds ? The secondary little problem: what is the mesurement unit of molar extinction coefficient in UV-VIS spectra graphs in CAChe 3.22 ? Is it the same unit that is used in this spectroscopy field ?
>>

With best regards,
Anatoly Goifman
The Hebrew University of Jerusalem
Phone: 972-2-6586260
Fax: 972-2-65856155
E-mail: tantra@pob.huji.ac.il
  --------------E15359ECEB2D061189D32A2A-- From chemistry-request@server.ccl.net Wed Dec 13 15:23:40 2000 Received: from mum.mans.eun.eg (mum.mans.eun.eg [193.227.50.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA19806 for ; Wed, 13 Dec 2000 15:23:32 -0500 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id ; Wed, 13 Dec 2000 22:26:06 +0200 Message-ID: <4EF2E03A9B67D2119E2E0000F80534994274D0@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'chemistry@ccl.net'" Subject: Aminothiazole x-ray data Date: Wed, 13 Dec 2000 22:26:05 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C06542.EB62B0E7" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C06542.EB62B0E7 Content-Type: text/plain Dear CCLERS Could any one give me or point me to a reference/database (free) where I can find the x-ray data for aminothiazole or 2-aminothiazole. Regards Tarek ------_=_NextPart_001_01C06542.EB62B0E7 Content-Type: text/html Content-Transfer-Encoding: quoted-printable Aminothiazole x-ray data

Dear CCLERS
Could any one give me or point me to = a reference/database (free) where I can find the x-ray data for = aminothiazole or 2-aminothiazole.

Regards
Tarek

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