From chemistry-request@server.ccl.net Mon May 20 20:45:33 2002 Received: from web12807.mail.yahoo.com ([216.136.174.42]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4L0jX126008 for ; Mon, 20 May 2002 20:45:33 -0400 Message-ID: <20020521004528.33455.qmail@web12807.mail.yahoo.com> Received: from [64.94.101.217] by web12807.mail.yahoo.com via HTTP; Mon, 20 May 2002 17:45:28 PDT Date: Mon, 20 May 2002 17:45:28 -0700 (PDT) From: amor san juan Subject: mol2 file format To: chemistry@ccl.net Cc: Ruth Huey MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello CCLers, Would someone please forward me the Sybyl mol2 file format description. Im having hard time figuring out in justifying the result I got in ben.pdbq which is different in data coordinates file of benA.pdbq sourced from file example distribution in AutoDock3. I need your help. Thanks in advance. Sincerely, Amor San Juan __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Tue May 21 03:22:43 2002 Received: from mx3.ust.hk ([143.89.13.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4L7Mg109506 for ; Tue, 21 May 2002 03:22:43 -0400 Received: from chz107 (chz107.ust.hk [143.89.53.152]) by mx3.ust.hk (8.12.2/8.12.2) with SMTP id g4L7Mc9X034747 for ; Tue, 21 May 2002 15:22:39 +0800 (HKT) From: "Zhenyang Lin" To: Subject: CASSCF Date: Tue, 21 May 2002 15:22:35 +0800 Message-ID: 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 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Colleagues, Recently, a referee to one of our manuscripts suggests that we perform 14-electrons-and-10MOs CASSCF calculations on the systems we have studied. We have trouble in performing the suggested type of CASSCF calcns within the G98 package. Does anyone have the experience of doing such big calcns with G98? Any comments and other suggestions will be greatly appreciated. Best wishes, Zhenyang Lin/Chemistry Hong Kong From chemistry-request@server.ccl.net Tue May 21 05:18:46 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4L9Ij114345 for ; Tue, 21 May 2002 05:18:45 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Tue, 21 May 2002 09:18:05 +0200 Message-ID: <001f01c20097$a9fe9250$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: References: <470C5643-6BF7-11D6-9B09-0050E4863261@wso.williams.edu> Subject: Re: CCL:bond lenghts Date: Tue, 21 May 2002 09:18:09 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 > On Monday, May 20, 2002, at 07:53 AM, Martijn Zwijnenburg wrote: > > > I'm looking for a program which can read in the structure of a > > molecule (as pdb or xyz) and output a table of bond-lengths (or > > atom-atom distances for what it's worth). No difficult analysis > > methods needed, just one structure. I'm thinking of an output like: Mol2Mol can calculate and output distances, angles and dihedrals in batch mode from a series of files or a multiple molecule file with the same structure, as shown: atoms in question are to be entered in this format: 87 70 32 31 34 32 31 34 45 44 46 49 50 46 49 50 51 output (for each molecule in the file): DIST 2.193 H(87)-H(70) PIM ANG 111.3 N(32)-C(31)-C(34) ALA DIH -13.6 N(32)-C(31)-C(34)-N(45) ALA DIH 57.5 C(44)-C(46)-C(49)-C(50) D_IG More about: http://www.compuchem.de/nutshell/index.html Here from the Contents select Main Window, then Utilities from the menu bar image and the last item, More geometry Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu From chemistry-request@server.ccl.net Tue May 21 06:05:04 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LA54116348 for ; Tue, 21 May 2002 06:05:04 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) id <0GWG00E01HCEY9@mailhost2.tudelft.nl> for chemistry@ccl.net; Tue, 21 May 2002 12:05:04 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) with ESMTP id <0GWG00D9XHCEBM@mailhost2.tudelft.nl> for chemistry@ccl.net; Tue, 21 May 2002 12:05:02 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g4LA52318878 for ; Tue, 21 May 2002 12:05:02 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Tue, 21 May 2002 12:05:02 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Tue, 21 May 2002 12:04:54 +0000 (MET-1MEST) Date: Tue, 21 May 2002 12:04:49 +0200 From: Martijn Zwijnenburg Subject: bond lenghts-summary In-reply-to: <3CE90DBE.19813.4314342A@localhost> To: chemistry@ccl.net Message-id: <3CEA37CF.15.47A08664@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal 0000,0000,0000Hi, Thanks for all the people who answered my question. There where to many to all thank individually. Summarizing the following programs should do the trick: A) Weblab viewer (from Accelerys), via the new data table option B) Babel, via the report data format < C) Project Leader from CAChe WS (Fujitsu) D) Zoa v2.0, http://zoa.freeservers.com E) MO package (like Gaussian), generate distance table F) via ScientificPhython, dirac.cnrs-orleans.fr/ScientifciPython/ Cheers Martijn0000,8000,0000 My original question 7F00,0000,0000> Hi, > > I'm looking for a program which can read in the structure of a > molecule (as pdb or xyz) and output a table of bond-lengths (or > atom-atom distances for what it's worth). No difficult analysis > methods needed, just one structure. I'm thinking of an output like: > > Si1-O4 1.644 > Si1-O5 1.643 > etc. etc. > > I can do this by hand in almost any viewer but since my molecules > are rather big I'm looking for a more efficient solution. > > Regards, > > Martijn Zwijnenburg > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg@tnw.tudelft.nl > web page: http://come.to/tock > > -= 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 > > > > > ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Tue May 21 06:38:09 2002 Received: from mailhub.cs.uoguelph.ca ([131.104.96.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LAc9117602 for ; Tue, 21 May 2002 06:38:09 -0400 Received: from ccshst01.cs.uoguelph.ca (ccshst01.cs.uoguelph.ca [131.104.96.81]) by mailhub.cs.uoguelph.ca (8.11.6/8.11.6) with ESMTP id g4LAc6l02852 for ; Tue, 21 May 2002 06:38:06 -0400 (EDT) Date: Tue, 21 May 2002 06:38:05 -0400 (EDT) From: Ruth Tanner X-Sender: rtanner@ccshst01.cs.uoguelph.ca To: chemistry@ccl.net Subject: Transition States with QCISD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I want to do transition state calculations with QCISD and I get the following error when I try to run my jobs: -------------------------------------------------------- #qcisd/6-311G** opt=(TS,NOEIGENTEST,CALCFC) freq pop=reg -------------------------------------------------------- No analytic 2nd derivatives for this method. Error termination via Lnk1e in /opt/g98/l1.exe. Is there a way around this problem? Ruth -------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca -------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue May 21 09:55:50 2002 Received: from mta02-svc.ntlworld.com ([62.253.162.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LDtn126690 for ; Tue, 21 May 2002 09:55:50 -0400 Received: from strath.ac.uk ([62.253.183.210]) by mta02-svc.ntlworld.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020521135549.JHIF4626.mta02-svc.ntlworld.com@strath.ac.uk>; Tue, 21 May 2002 14:55:49 +0100 Message-ID: <3CEA523F.A5F53638@strath.ac.uk> Date: Tue, 21 May 2002 14:57:19 +0100 From: "Dr. Peter Bladon" X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Rafael R. Pappalardo" CC: Jim Kress , chemistry@ccl.net Subject: Re: CCL:CHELP sources. References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I wonder if this is not a case of stuff being downloaded in the wrong format (windows versus unix). I have just tried downloading some files from the ccl archives. (1) I established an ftp connection (not http) by doing: ftp www.ccl.net (logiing in as anonymous in the usual way) (2)then: cd pub/chemistry/coftware/SOURCES/FORTRAN/chelpg (3) Then: get chelpgunix.f The file which was download in "binary" mode was readable on my IRIX machine I have just done the same on a Windows machine but I switched to "ASCII" mode instead of "bin" mode before downloading the file. Again the file was readable and had the correct format Significantly, the windows file was longer (208766 bytes) than the file on the Unix machine (206220 bytes) the extra length being due to the extra "carriage returns" (ASCII code 13) needed by DOS/windows systems. It is relatively easy to reformat between the two systems provided you have access to a Unix machine using the utilities to_unix and to_dos. But I do not know how to do it on a Windows machine??? Hope this helps Peter Bladon "Rafael R. Pappalardo" wrote: > > On Mon, 20 May 2002, Jim Kress wrote: > > > Why don't you ask the author? Follow this link: > > > > http://www.brynmawr.edu/chemistry/mfrancl.html > > > > Jim > > > > Sorry, I forgot to mention that I sent mails to both of > them without success. > > Rafael > > > > ----- Original Message ----- > > From: "Rafael R. Pappalardo" > > To: > > Sent: Monday, May 20, 2002 10:55 AM > > Subject: CCL:CHELP sources. > > > > > > > Dear all, > > > > > > I am trying to implement the CHELP method in some ab initio code. > > > I have downloaded the sources from > > > > > > http://www.ccl.net/cca/software/SOURCES/FORTRAN/chelpg/new/ > > > > > > directory. Surprisingly the files have lost the fortran format. > > > The lines begin at column 1. Some continuation lines are merged > > > together, etc. > > > > > > The gopher address mentioned does not work anymore. QCPE list the > > > program as not available. > > > > > > Does anybody knows where to get it? It will be wonderfull if it is a > > > version including latest recommendations from Profs. Francl and Chirlian > > > (RCC vol 14). > > > > > > Thanks, > > > > > > -- > > > Dr. Rafael R. Pappalardo > > > Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla > > (Spain) > > > e-mail: rafapa@simulux.us.es > > > > > > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > > Admins > > > 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. Rafael R. Pappalardo > Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) > e-mail: rafapa@simulux.us.es > > -= 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 Tue May 21 10:11:50 2002 Received: from simulux.us.es (IDENT:root@[150.214.145.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LEBo127479 for ; Tue, 21 May 2002 10:11:50 -0400 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.8.7) with ESMTP id QAA06977; Tue, 21 May 2002 16:12:58 +0200 Date: Tue, 21 May 2002 16:12:58 +0200 (CEST) From: "Rafael R. Pappalardo" To: "Dr. Peter Bladon" cc: Jim Kress , Subject: Re: CCL:CHELP sources. In-Reply-To: <3CEA523F.A5F53638@strath.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 21 May 2002, Dr. Peter Bladon wrote: > I wonder if this is not a case of stuff being downloaded in the wrong > format (windows versus unix). > > I have just tried downloading some files from the ccl archives. > > (1) I established an ftp connection (not http) by doing: > ftp www.ccl.net (logiing in as anonymous in the usual way) > > (2)then: > cd pub/chemistry/coftware/SOURCES/FORTRAN/chelpg > > (3) Then: > get chelpgunix.f > > The file which was download in "binary" mode was readable on my IRIX > machine > > I have just done the same on a Windows machine but I switched to "ASCII" > mode > instead of "bin" mode before downloading the file. > Again the file was readable and had the correct format > > Significantly, the windows file was longer (208766 bytes) than the > file on the Unix machine (206220 bytes) the extra length being due to > the > extra "carriage returns" (ASCII code 13) needed by DOS/windows systems. > > It is relatively easy to reformat between the two systems provided you > have access to a Unix machine using the utilities to_unix and to_dos. > But I do not know how to do it on a Windows machine??? > > Hope this helps > > Peter Bladon > Dear Peter, the problem is not with files in the chelpg directory but with the files in the new directory. They seem to have been sent by e-mail and I suspect they got corrupted. Could you please verify if you can get working Fortran files from the new directory? Best regards, Rafael -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Tue May 21 13:31:57 2002 Received: from access.etsu.edu ([151.141.99.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LEnO129123 for ; Tue, 21 May 2002 10:49:24 -0400 Received: from dmc.etsu.edu ([151.141.29.51]) by ACCESS.ETSU.EDU (PMDF V6.1 #39282) with ESMTP id <01KHZJDIEFLC99FNZ5@ACCESS.ETSU.EDU> for chemistry@ccl.net; Tue, 21 May 2002 10:49:05 -0400 (EDT) Date: Tue, 21 May 2002 10:50:08 -0400 From: David Close Subject: OVGF X-Sender: closed@access.etsu.edu To: chemistry@ccl.net Message-id: <5.1.0.14.1.20020521103745.02411bc0@access.etsu.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7BIT CCL: Last month I requested help with calculating IP's with the OVGF options in G98. I received several e-mails asking for a summary. I was able to solve the problem with help from Vince Ortiz and Jim Hess. Both thought that there may be something wrong with my version of G98 for LINUX (revision 7.) I bought revision 11 and installed it. I can now do these calculations. I must say that I do not know what was actually wrong with revision 7. These calculations involve lots of disc space and at the start I did not have enough disc space in the work area I was using. This was all taken care of with a memo from Gaussian about G98 memory and disk space. Thanks to those who helped. Regards, Dave Close. From chemistry-request@server.ccl.net Tue May 21 09:53:32 2002 Received: from post.webmailer.de ([192.67.198.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LDrV126556 for ; Tue, 21 May 2002 09:53:32 -0400 Received: from fepa.biop.ox.ac.uk (fepa.biop.ox.ac.uk [163.1.16.72]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id PAA26007 for ; Tue, 21 May 2002 15:53:20 +0200 (MEST) Message-Id: <200205211353.PAA26007@post.webmailer.de> X-Mailer: exmh version 2.3.1 01/18/2001 (debian 2.3.1-1) with nmh-1.0.2 To: CHEMISTRY@ccl.net Subject: Why should one scale charges down for implicit solvent calculations ? X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Tue, 21 May 2002 14:51:59 +0100 From: Marc Baaden Dear colleagues, I re-iterate my question about charge scaling, as I have received 3 requests for summaries, but no replies. So if you have any comments on this, or would in any other way like to contribute (eg stimulate a discussion ?), please do so. Here is the original question: I am trying to get hold of a sound reference, providing a rationale for scaling the charges of ionized groups when doing implicit solvent calculations (MM, MD, NMA) with eg epsilon=80 or epsilon=f(r). I am roughly aware of the counterion condensation theory of Manning and related work, but am not sure whether this is the only argument for charge scaling. Scaling factors (for proteins !) that I have seen in the literature seem to be around eg 0.3. How are they derived (ad hoc ? or by using the Xi=1 relation of Manning and calculating the charge density of the molecule). Also Manning's work focused on simple cylindrical models of polyions, but I am particularly interested in proteins. Is there any work focusing on this problem ? Thanks in advance, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Tue May 21 09:46:35 2002 Received: from tucc-exchange.trinity.edu ([131.194.151.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LDkY126195 for ; Tue, 21 May 2002 09:46:34 -0400 Received: by tucc15.tucc.trinity.edu with Internet Mail Service (5.5.2653.19) id ; Tue, 21 May 2002 08:44:50 -0500 Message-ID: From: "Bachrach, Steven" To: "'Mark Thompson'" , ajc@dq.ufscar.br, chemistry@ccl.net Subject: RE: ZINDO Date: Tue, 21 May 2002 08:44:49 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Just a minor correction here, GAUSSIAN is available as source code, a feature that gets often overlooked, and quite unusual among the commercial suppliers of codes. Steve -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 715 Stadium Drive San Antonio, TX 78212 steven.bachrach@trinity.edu > -----Original Message----- > From: Mark Thompson [mailto:planaria@seanet.com] > Sent: Monday, May 20, 2002 6:01 AM > To: ajc@dq.ufscar.br; chemistry@ccl.net > Subject: CCL:ZINDO > > > Dear Ademir, > > The original ZINDO program from the Zerner group is now commercially > distributed by Accelrys. To my knowledge the source is not > publicly available, > nor am I certain how well Accelrys is maintaining the code > (it was very > difficult to maintain and enhance). > > Other sources of ZINDO capability are (in alphabetical order): > > 1. ArgusLab (http://www.arguslab.com) > 2. CAChe > 3. Gaussian > 4. HyperChem > > All of the above are commercial programs and not available in > source form as > far as I know. > > Cheers, > Mark > > > > Dear CCL'ers, > > > > I am very interested in a free source code for the ZINDO > program. Known > > any one if such a copy is available for the public domain? > > > > Thanks in advance, > > > > Dr. Ademir Camargo > > > > > > > > > > > > > > > > > > > > > ======================================= > Mark Thompson, Ph.D. > Planaria Software > Seattle, WA > > http://www.arguslab.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 Tue May 21 08:54:35 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LCsZ123588 for ; Tue, 21 May 2002 08:54:35 -0400 Received: from humagne.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g4LCsVx20995 for ; Tue, 21 May 2002 14:54:31 +0200 (MEST) Received: (from portmann@localhost) by humagne.ethz.ch (8.11.4/8.11.4) id g4LCsVB08214 for chemistry@ccl.net; Tue, 21 May 2002 14:54:31 +0200 (MEST) Date: Tue, 21 May 2002 14:54:31 +0200 (MEST) Message-Id: <200205211254.g4LCsVB08214@humagne.ethz.ch> From: Stefan Portmann Reply-To: info@watoc02.ch Subject: WATOC'02: Last Call for Contributions! Content-Type: text Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science Last Call for Contributions! Please submit an abstract for your contribution until the end of May using the online form at http://www.watoc02.ch (Deadline: May 31, 2002). In order to give the poster sessions optimal visibility, an award program was established. The posters will be rated both on popular and on jury votes. There will be a two hour award ceremony on Thursday evening. The poster sessions will be endowed by Gaussian, Inc.. To register and for program informations please check http://www.watoc02.ch. Registrations are accepted until June 14, 2002. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Tue May 21 13:34:55 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LH1t103455 for ; Tue, 21 May 2002 13:01:55 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id NAA321668 for ; Tue, 21 May 2002 13:01:54 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: CHEMISTRY@ccl.net Subject: q question regarding a structure Date: Tue, 21 May 2002 13:00:28 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200205211300.28268.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I've been trying to look for the structure (and CAS number) of o,s diethyl methyl phosphonothlolate I've looked on the free online databases as well as the CAS substance index, but I could'nt find anything. I'd appreicate it if anybody who knows the structure and/or CAS number could let me know. TIA., - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- Love is like the measles; we all have to go through it. -- Jerome K. Jerome -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE86n0szcRVdJAXryoRAq7OAJ9ugs5MOriwnoRGXNi+58kd87LY7wCbB0vd 14fk7vI2dU99sK0bmZUit1s= =pCNL -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Tue May 21 13:35:00 2002 Received: from thunderer.cnchost.com ([207.155.252.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LGdP102204 for ; Tue, 21 May 2002 12:39:26 -0400 Received: from guillermo ([63.127.188.98]) by thunderer.cnchost.com id MAA18411; Tue, 21 May 2002 12:39:14 -0400 (EDT) [ConcentricHost SMTP Relay 1.14] Errors-To: Reply-To: From: "Dr. Guillermo A. Morales" To: "amor san juan" , Cc: "Ruth Huey" Subject: RE: mol2 file format Date: Tue, 21 May 2002 09:38:27 -0700 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal In-Reply-To: <20020521004528.33455.qmail@web12807.mail.yahoo.com> X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 You can find this information at Tripos' site: http://www.tripos.com/services/mol2/ I hope this helps. Best, - Guillermo. ----- Dr. Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of amor san juan Sent: Monday, May 20, 2002 5:45 PM To: chemistry@ccl.net Cc: Ruth Huey Subject: CCL:mol2 file format Hello CCLers, Would someone please forward me the Sybyl mol2 file format description. Im having hard time figuring out in justifying the result I got in ben.pdbq which is different in data coordinates file of benA.pdbq sourced from file example distribution in AutoDock3. I need your help. Thanks in advance. Sincerely, Amor San Juan __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.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 Tue May 21 05:23:18 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4L9NH114557 for ; Tue, 21 May 2002 05:23:18 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 17AEJT-00024J-00 for chemistry@ccl.net; Tue, 21 May 2002 11:24:47 -0700 Date: Tue, 21 May 2002 10:26:13 +0200 (CEST) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: chemistry@ccl.net Subject: FF for small molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'd like to know your opinion about the best FF for simulate interaction betwenn small molecules (like organic molecule, H2O, CH4, drugs ecc) -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it RESISTERE RESISTERE RESISTERE ... From chemistry-request@server.ccl.net Tue May 21 07:15:47 2002 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LBFk119047 for ; Tue, 21 May 2002 07:15:47 -0400 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id NAA20536 for ; Tue, 21 May 2002 13:15:31 +0200 (MET DST) Message-ID: <003601c200b8$f5695a60$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: question about the CHOOSE keyword in NBO Date: Tue, 21 May 2002 13:16:29 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01C200C9.B828BFE0" 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_0033_01C200C9.B828BFE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I have a doubt about the operation of analysis NBO searching the best = Lewis structure. The description of Lewis of a certain molecule gives me a little strange = result. Then I repeat the calculation on the same molecule with the = option CHOOSE (DIRECTED NBO SEARCH) choosing a more "normal" structure = of Lewis and in this second calculation I obtain a smaller Dev and = smaller Total non-Lewis.=20 This is normal? Because I thought that in the process of optimization = NBO the structure with a smaller amount of non-Lewis and a smaller Dev = would have to be obtained. Thanks ******************************************* Without CHOOSE (free NBO search): ******************************************* NATURAL BOND ORBITAL ANALYSIS: Cycle Thresh. Lewis Non-Lewis CR BD 3C LP (L) (NL) Dev =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D 1(1) 1.90 33.82805 2.17195 5 11 0 2 2 3 0.59 2(2) 1.90 33.82805 2.17195 5 11 0 2 2 3 0.59 3(1) 1.80 34.34760 1.65240 5 12 0 1 2 3 0.59 4(2) 1.80 33.42460 2.57540 5 13 0 0 4 5 0.59 . . 38(9) 1.50 34.21710 1.78290 5 11 0 2 1 3 0.37 39(1) 1.70 34.54664 1.45336 5 12 0 1 1 3 0.37 -------------------------------------------------------------------------= ---- Total non-Lewis 1.45336 ( 4.037% of 36) -------------------------------------------------------- ******************* With CHOOSE: ******************* NATURAL BOND ORBITAL ANALYSIS: Cycle Thresh. Lewis Non-Lewis CR BD 3C LP (L) (NL) Dev =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D 1(1) 1.90 34.72964 1.27036 5 12 0 1 3 3 0.34 -------------------------------------------------------------------------= ---- Total non-Lewis 1.27036 ( 3.529% of 36) ------=_NextPart_000_0033_01C200C9.B828BFE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi

I have a doubt about the operation of analysis NBO searching the best = Lewis=20 structure.

The description of Lewis of a certain molecule gives me a little = strange=20 result. Then I repeat the calculation on the same molecule with the = option=20 CHOOSE (DIRECTED NBO SEARCH) choosing a more "normal" structure of Lewis = and in=20 this second calculation I obtain a smaller Dev and smaller Total = non-Lewis.

This is normal? Because I thought that in the process of optimization = NBO the=20 structure with a smaller amount of non-Lewis and a smaller Dev would = have to be=20 obtained.

Thanks

 

*******************************************
Without CHOOSE (free NBO search):
*******************************************
NATURAL BOND ORBITAL ANALYSIS:
 
Cycle Thresh. Lewis Non-Lewis CR BD 3C LP (L) (NL) Dev
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D
1(1) 1.90 33.82805 2.17195 5 11 0 2 2 3 0.59
2(2) 1.90 33.82805 2.17195 5 11 0 2 2 3 0.59
3(1) 1.80 34.34760 1.65240 5 12 0 1 2 3 0.59
4(2) 1.80 33.42460 2.57540 5 13 0 0 4 5 0.59
.
.
38(9) 1.50 34.21710 1.78290 5 11 0 2 1 3 0.37
39(1) 1.70 34.54664 1.45336 5 12 0 1 1 3 = 0.37
--------------------------------------------------------------------= ---------
Total non-Lewis 1.45336 ( 4.037% of 36)
--------------------------------------------------------
 
 
*******************
With CHOOSE:
*******************
NATURAL BOND ORBITAL ANALYSIS:
 
Cycle Thresh. Lewis Non-Lewis CR BD 3C LP (L) (NL) Dev
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D
1(1) 1.90 34.72964 1.27036 5 12 0 1 3 3 0.34
--------------------------------------------------------------------= ---------
 
Total non-Lewis 1.27036 ( 3.529% of=20 36)
 ------=_NextPart_000_0033_01C200C9.B828BFE0-- From chemistry-request@server.ccl.net Tue May 21 17:23:57 2002 Received: from zimail1.unizh.ch ([130.60.128.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LLNv012041 for ; Tue, 21 May 2002 17:23:57 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.68.15]) by zimail1.unizh.ch (8.12.1/8.12.1/smMTA-12) with ESMTP id g4LLNuTI000477 for ; Tue, 21 May 2002 23:23:57 +0200 (MEST) Date: Tue, 21 May 2002 23:23:56 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: COSMO & TDDFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, title says it all. I am searching for codes that allow to combine TDDFT and COSMO, which afaik my favourite program Turbomole cannot deal with. Regards, Peter ---------------------------- Peter Burger University of Zuerich From chemistry-request@server.ccl.net Tue May 21 09:08:47 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LD8k124308 for ; Tue, 21 May 2002 09:08:46 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id QAA07487; Tue, 21 May 2002 16:08:40 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Tue, 21 May 2002 16:08:40 +0300 (EET DST) From: Mikael Johansson X-Sender: To: amor san juan cc: Subject: Re: CCL:mol2 file format In-Reply-To: <20020521004528.33455.qmail@web12807.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Amor and All! On Mon, 20 May 2002, amor san juan wrote: > Would someone please forward me the Sybyl mol2 file > format description. Im having hard time figuring out > in justifying the result I got in ben.pdbq which is > different in data coordinates file of benA.pdbq > sourced from file example distribution in AutoDock3. You can (surprisingly ;-) find it at the Tripos home page: http://www.tripos.com/services/mol2/ Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@server.ccl.net Tue May 21 15:47:27 2002 Received: from jacobus.chem.smu.edu ([129.119.201.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LJlQ007396 for ; Tue, 21 May 2002 15:47:27 -0400 Received: from localhost (zmz@localhost) by jacobus.chem.smu.edu (8.11.6/8.11.6) with ESMTP id g4LJeKO10615 for ; Tue, 21 May 2002 14:40:20 -0500 Date: Tue, 21 May 2002 14:40:20 -0500 (CDT) From: Pearl Zheng To: Subject: FlexX help needed Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi dear CCL users, I am using sybyl FlexX to docking a small molecule to the active site of an enzyme. But the assignment of formal charges automatically by FlexX only works well in simple case. My question is how can I assign formal charge by myself. The second question is can I use Gasteiger-Huckel charges while doing FlexX? All response are appreciated. ---Mingzhu From chemistry-request@server.ccl.net Tue May 21 18:39:06 2002 Received: from trivial.uchicago.edu (IDENT:root@[128.135.160.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LMd6015249 for ; Tue, 21 May 2002 18:39:06 -0400 Received: from localhost (cmtaylor@localhost) by trivial.uchicago.edu (8.9.3/8.9.3) with ESMTP id RAA10249 for ; Tue, 21 May 2002 17:39:03 -0500 Date: Tue, 21 May 2002 17:39:03 -0500 (CDT) From: Caroline Taylor To: CHEMISTRY@ccl.net Subject: ccsd in g98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there. I was wondering if anyone had a feel for how reliable the CCSD implementation in Gaussian98 is for open shell systems? We're seeing some odd results, and I'd like to rule this out as a problem. Thanks! -Caroline -- --------------------------------------------- Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 --------------------------------------------- From chemistry-request@server.ccl.net Tue May 21 15:40:41 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LJef007083 for ; Tue, 21 May 2002 15:40:41 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id PAA21470; Tue, 21 May 2002 15:40:32 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 21 May 2002 15:38:16 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GWH00ECV7PO9T@lvlmail.unitedcatalysts.com>; Tue, 21 May 2002 15:34:36 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 21 May 2002 15:38:01 -0400 Content-return: allowed Date: Tue, 21 May 2002 15:37:57 -0400 From: "Shobe, Dave" Subject: RE: Re:g98 Symmetry To: "'Roma Oakes'" , ccl Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15CDA@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 g4LJef007084 Usually the "Omega: " message is enough to kill the job. What it means (anthropomorphically speaking!) is that Gaussian realizes that it has to switch the x and y axes (or some similar operation), but is too dumb to actually do it. I wish Gaussian would fix this but I'm not holding my breath. --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. -----Original Message----- From: Roma Oakes [mailto:r.e.oakes@btconnect.com] Sent: Sunday, May 19, 2002 3:34 PM To: ccl Subject: CCL:Re:g98 Symmetry Dear All thanks to all who responded to my question about symmetry in G98. I have been sent a few files, some with C2 symmetry and one with D2, I'll be trying them all, but they have certainly helped a lot. Mind you, one of the jobs (that had started with C2 symmetry) had been going along very well when it crashed with; (I had used iop(2/17=1, 2/16=3) Leave Link 103 at Sun May 19 17:48:29 2002, MaxMem= 73400320 cpu: 51.0 (Enter C:\G98W\l202.exe) Stoichiometry C36H46N4 Framework group D2[C2'(N.N),C2"(NH.HN),X(C36H44)] Deg. of freedom 63 Full point group D2 NOp 4 Omega: Change in point group or standard orientation. Largest Abelian subgroup D2 NOp 4 Largest concise Abelian subgroup D2 NOp 4 Operation on file out of range. FileIO: IOper= 1 IFilNo(1)= -579 Len= 172 IPos= 0 Q= 56304400 (a lot of stuff about dumping files) Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO. I've restarted it but don't really know what the error means Regards Roma -= 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 Tue May 21 16:48:06 2002 Received: from mail.cambridgesoft.com ([198.112.109.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LKm6010104 for ; Tue, 21 May 2002 16:48:06 -0400 Received: from 172.16.1.10 by mail.cambridgesoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.3); 21 MAY 02 16:47:55 UT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: Jonathan Brecher@mail.camsoft.com Message-Id: In-Reply-To: <200205211300.28268.rajarshi@presidency.com> Date: Tue, 21 May 2002 16:47:51 -0400 To: CHEMISTRY@ccl.net From: Jonathan Brecher Subject: Re: CCL:q question regarding a structure > I've been trying to look for the structure (and CAS number) of > >o,s diethyl methyl phosphonothlolate > >I've looked on the free online databases as well as the CAS substance index, >but I could'nt find anything. That's not surprising, since the name is incompletely specified and has at least one additional typo. You have three ligands (ethyl, ethyl, methyl), but only two locants (O, S). There's a typo somewhere. If I had to guess, I'd speculate that you're looking for O,S-diethyl O-methyl phosphonothioate, which is clearly P(=O)(OCC)(SCC)OC -- but that's strictly a guess based on incomplete information. There's roughly a dozen other substances that you might be looking for, depending on the actual resolution of the typos. Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com From chemistry-request@server.ccl.net Tue May 21 14:08:47 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4LI8k002735 for ; Tue, 21 May 2002 14:08:47 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 17AMW3-0002vp-00 for chemistry@ccl.net; Tue, 21 May 2002 20:10:19 -0700 Date: Tue, 21 May 2002 19:11:46 +0200 (CEST) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: chemistry@ccl.net Subject: FF for small molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'like to know about how standard molecular force fields can predict bond and non-bond interactions in organic molecules (like drugs, small molecules, ecc). wich is the best to predict energy of a complex? wich is the best to predict VdW forces? wich is the best to predict MEP? could any of you give me reference about comparation between differents force fields? thanks in advance -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it RESISTERE RESISTERE RESISTERE ...