From CHEM8@vax.york.ac.uk Sat Mar 4 07:10:02 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA26572; Sat, 4 Mar 1995 06:24:39 -0500 Via: uk.ac.york.vax; Sat, 4 Mar 1995 11:20:00 +0000 Date: Sat, 4 Mar 95 11:21 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Problem with SGI 'Explorer' using another X-terminal. Message-ID: <"leeman.yor.785:04.02.95.11.20.02"@york.ac.uk> Hi Netters, I have been asked to find out whether anyone has come up agaigst the following problem and solved it. If so how (apart from buying an SGI terminal)? For example, should an SGI emulator be used and if so where can one get such software? An SGI 'Crimson' is available which has the package 'Explorer'. When these routines are run from the console, an SGI X-terminal, it works fine. However, when other, colour X-terminals, HPs specifically, are used to run this program, connected through an ethernet, the window that should contain the final display (results) remains blank and the following messages are obtained: > > Warning: Color name "sgigray76" is not defined in server database > Warning: Cannot convert string "InsertChar " to type VirtualBinding > Warning: Cannot convert string "DeleteChar " to type VirtualBinding > Warning: Cannot convert string "InsertLine " to type VirtualBinding > Warning: Cannot convert string "DeleteLine " to type VirtualBinding > Warning: Color name "sgiteal" is not defined in server database > Warning: Color name "sgigray84" is not defined in server database > Warning: Color name "sgigray52" is not defined in server database > Render: Warning: Color name "sgigray76" is not defined in server database > Render: Warning: Cannot convert string "InsertChar " to type VirtualBinding > Render: Warning: Cannot convert string "DeleteChar " to type VirtualBinding > Render: Warning: Cannot convert string "InsertLine " to type VirtualBinding > Render: Warning: Cannot convert string "DeleteLine " to type VirtualBinding > Other programs run satisfactorily on the Crimson using HP, X-terminals. As SGI only have a representative other here I think it would be useful if we could get in contact with SGI, US or Europe. Any help on this will be much appreciated, John Waite From o.casher@ic.ac.uk Sat Mar 4 08:09:32 1995 Received: from romeo.ic.ac.uk for o.casher@ic.ac.uk by www.ccl.net (8.6.10/930601.1506) id HAA27040; Sat, 4 Mar 1995 07:57:08 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Sat, 4 Mar 1995 12:56:47 +0000 Received: from [155.198.224.115] by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA11804; Sat, 4 Mar 95 12:56:26 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 4 Mar 1995 12:56:15 +0000 To: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" From: o.casher@ic.ac.uk (Omer Casher) Subject: Re: CCL:Problem with SGI 'Explorer' using another X-terminal. Cc: chemistry@ccl.net > Hi Netters, > I have been asked to find out whether anyone has come up agaigst the > following problem and solved it. If so how (apart from buying an SGI >terminal)? > For example, should an SGI emulator be used and if so where can one get such > software? > An SGI 'Crimson' is available which has the package 'Explorer'. When > these routines are run from the console, an SGI X-terminal, it works fine. > However, when other, colour X-terminals, HPs specifically, are used to run > this program, connected through an ethernet, the window that should contain > the final display (results) remains blank and the following messages are > obtained: [ Explorer error stuff deleted ] I've only succeeded in doing this between two SGIs. Without getting technical, if you want to render your model on a non SGI X-terminal it must have OpenGL (in theory, at least). > Other programs run satisfactorily on the Crimson using HP, X-terminals. > As SGI only have a representative other here I think it would be useful > if we could get in contact with SGI, US or Europe. Check out http://www.nag.co.uk/0/visual/IE/iecbb/Product.html for more help. BTW, have you considered acquiring an HP port of Explorer? Hope this is of some use. Omer From MB@CHEM.UNI.WROC.PL Sat Mar 4 09:09:33 1995 Received: from for MB@CHEM.UNI.WROC.PL by www.ccl.net (8.6.10/930601.1506) id IAA27206; Sat, 4 Mar 1995 08:17:19 -0500 Received: from ichuwr.chem.uni.wroc.pl by hera.math.uni.wroc.pl with SMTP (1.38.193.4/16.2) id AA07867; Sat, 4 Mar 1995 14:10:53 +0100 Received: from ICHUWR/SMTPQueue by chem.uni.wroc.pl (Mercury 1.11); Sat, 4 Mar 95 14:19:48 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Sat, 4 Mar 95 14:19:45 +0100 From: "Malgorzata Biczysko" To: chemistry@ccl.net Date: Sat, 4 Mar 1995 14:19:40 GMT+1 Subject: CCL: Topological Index X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail v3.1 (R1) Message-Id: <2B7D61A6942@chem.uni.wroc.pl> Hi netters, I want to do some QSAR research and I'm looking for any free program to calculate any topological (graph-theoretical) indices (eg. Randic index, Wiener index, Balaban index and so one). thanks Malgorzata Biczysko From U13145@UICVM.CC.UIC.EDU Sat Mar 4 10:09:30 1995 Received: from phem3 for U13145@UICVM.CC.UIC.EDU by www.ccl.net (8.6.10/930601.1506) id JAA27560; Sat, 4 Mar 1995 09:42:33 -0500 Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HNQF5Z2KHS98BLB6@phem3.acs.ohio-state.edu>; Sat, 4 Mar 1995 09:42:28 EST Received: from UICVM (NJE origin U13145@UICVM) by UICVM.CC.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 6308; Sat, 4 Mar 1995 08:42:02 -0600 Date: Sat, 04 Mar 1995 08:31:38 -0600 (CST) From: U13145%UICVM.BITNET@phem3.acs.ohio-state.edu Subject: pKa of reduced amide bond N To: CHEMISTRY@ccl.net Message-id: <01HNQF5Z2KHU98BLB6@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I am modeling peptide mimetics which include a reduced peptide bond. The isosteric (CH2NH) sp3 N may be protonated under tested biological conditions. I was wondering if anyone can help me with a pKa value either theoretical or experimental for this type of nitrogen. A pKa value for protonated dimethyl ammonium NH2+(CH3)2 would suffice as an approximation. Thanks in advance for any help. John S. Tokarski Laboratory of Molecular Modeling and Design College of Pharmacy Univ. of Illinois at Chicago 833 S. Wood St., m/c 781, #539 Chicago, Il 60612 (312)996-6004 e-mail: u13145@uicvm.uic.edu fax: (312) 996-7107 From gilson@indigo14.carb.nist.gov Sat Mar 4 12:09:33 1995 Received: from ENH.NIST.GOV for gilson@indigo14.carb.nist.gov by www.ccl.net (8.6.10/930601.1506) id LAA28012; Sat, 4 Mar 1995 11:14:46 -0500 Received: from indigo14.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HNQICB42Q80011JV@ENH.NIST.GOV>; Sat, 4 Mar 1995 11:13:05 EST Received: by indigo14.carb.nist.gov (931110.SGI/930416.SGI) for @enh.nist.gov:chemistry@ccl.net id AA07460; Sat, 4 Mar 95 11:10:40 -0500 Date: Sat, 04 Mar 1995 11:10:40 -0500 From: gilson@indigo14.carb.nist.gov (Michael K. Gilson) Subject: Threat to the Internet To: chemistry@ccl.net Message-id: <9503041610.AA07460@indigo14.carb.nist.gov> Content-transfer-encoding: 7BIT There is a proposed regulation pending in the US Senate: (Senate Bill S.314) -- "Communications Decency Act". If passed, this bill would make organizations which provide Internet access to their employees or customers legally liable for the Internet materials originating at their site. If the bill passes, it will mean severe restrictions and censorship of all your electronic communications at the intracompany as well as government level. This would make using the Internet more difficult than sending a traditional letter by US Mail. To find more about the proposed regulation, and how you can protest its passing, please retrieve the concise summary from the CCL archives by sending a message: select chemistry get legal/senate314 to MAILSERV@ccl.net. Mike Gilson gilson@indigo14.carb.nist.gov From AGXSG@nasagiss.giss.nasa.gov Sat Mar 4 14:09:46 1995 Received: from NASAGISS.GISS.NASA.GOV for AGXSG@nasagiss.giss.nasa.gov by www.ccl.net (8.6.10/930601.1506) id NAA29222; Sat, 4 Mar 1995 13:49:15 -0500 Message-Id: <199503041849.NAA29222@www.ccl.net> Received: from NASAGISS.GISS.NASA.GOV by NASAGISS.GISS.NASA.GOV (IBM VM SMTP V2R2) with BSMTP id 5070; Sat, 04 Mar 95 13:50:42 EST Received: from nasagiss.giss.nasa.gov (AGXSG) by NASAGISS.GISS.NASA.GOV (Mailer R2.08) with BSMTP id 7956; Sat, 04 Mar 95 13:50:41 EST Date: Sat, 04 Mar 95 13:32:37 EST From: Sheldon Green Subject: nonreactive molecular dynamics code (MOLSCAT) To: chemistry@ccl.net X-Acknowledge-To: MOLSCAT is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem. It is developed and maintained jointly by myself and Jeremy Hutson. The current code is Version 14. Code is in near standard FORTRAN 77 and has been ported successfully to many hardware platforms. It is reasonably well documented and test input/output files are provided. The code is freely available for distribution via anonymous ftp or -- with a much friendlier user interface -- via the World Wide Web. Anonymous ftp files are at molscat.giss.nasa.gov in directory pub/molscat. The Web URL is http://molscat.giss.nasa.gov/MOLSCAT/ The Web site also has a user tutorial and full documentation, both available in hypertext mark-up language. Any problems or questions can be directed to Sheldon Green, agxsg@giss.nasa.gov From chiremv!andromeda!jeffb@uunet.uu.net Sat Mar 4 11:22:47 1995 Received: from relay3.UU.NET for chiremv!andromeda!jeffb@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id LAA28049; Sat, 4 Mar 1995 11:22:45 -0500 Received: from uucp6.UU.NET by relay3.UU.NET with SMTP id QQyfpx15333; Sat, 4 Mar 1995 11:22:51 -0500 Received: from chiremv.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Sat, 4 Mar 1995 11:22:45 -0500 Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA13655; Thu, 2 Mar 95 18:41:55 PST Received: by andromeda (931110.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry-request id AA18456; Thu, 2 Mar 95 18:22:22 -0800 Date: Thu, 2 Mar 95 18:22:22 -0800 From: chiremv!andromeda!jeffb@uunet.uu.net (Jeff Blaney) Message-Id: <9503030222.AA18456@andromeda> To: uunet!ccl.net!chemistry@uunet.uu.net Subject: Re: CCL:Conformational Analysis Status: R > I have been working with steroid conformational analysis in connection > with receptor modeling. I have generated several (typically 100) structures > (conformers) for each steroid using DGEOM program. Now I need to pick out > those conformers that are unique. (DGEOM generated structures might converge > to same minimum upon minimization). Any ideas on how to do that using > commercial modeling software or other shareware programs? The new release of DGEOM (DGEOM95) contains an option to filter conformations based on RMS deviation. There is also a new version of COMPARE (supplied with DGEOM95) which uses Jarvis-Patrick clustering to cluster conformers based on RMS deviation. You can use either approach to generate a unique set of conformers to an arbitrary cutoff based on RMS. Jeff Blaney Chiron