From byw@novo.dk Thu Aug 10 03:33:39 1995 Received: from sentry.novo.dk for byw@novo.dk by www.ccl.net (8.6.10/930601.1506) id DAA21829; Thu, 10 Aug 1995 03:25:51 -0400 Received: from bach.novo.dk by sentry.novo.dk; (5.65/1.1.8.2/28Sep94-0345PM) id AA26291; Thu, 10 Aug 1995 09:25:53 +0200 Received: by bach (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id JAA27701; Thu, 10 Aug 1995 09:23:35 +0200 Date: Thu, 10 Aug 1995 09:23:35 +0200 From: byw@novo.dk (Robert Bywater) Message-Id: <199508100723.JAA27701@bach> To: chemistry@ccl.net Subject: large output files Devapriya Choudhury asks : >Where can I find code (preferably in FORTRAN) which can do pairwise >superimposition of around 5000 molecules ( each having less than 20 atoms >and give the RMSE for each pair. --- Dear Dr. Choudhury --- Superimposing molecules ( molecular skeletons, I presume ) is --- an easy task in principle - one of the best methods is the --- quaternion method of A.L. Mackay in Acta. Cryst. (1984) A40 --- 165-166. It is not a difficult task to write a program to --- do this calculation in e.g. FORTRAN. But you have set yourself --- a massive task if you want to calculate RMSE's for each pair --- out of a family of 5000 compounds. If you want to store the --- results on one line of text ( 80 characters ) for each --- pair you will need something like 12497500 * 160 bytes of --- storage or approx. 2 GB. Good luck ! Robert Bywater ****************************** * * * Robert Bywater * * * * Biostructure Department * * NOVO NORDISK A/S * * * * DK-2880 BAGSVAERD Denmark * * * * email byw@novo.dk * * fax :: +45 4442 1400 * ****************************** ****************************** * * * Robert Bywater * * * * Biostructure Department * * NOVO NORDISK A/S * * * * DK-2880 BAGSVAERD Denmark * * * * email byw@novo.dk * * fax :: +45 4442 1400 * ****************************** From rickr@scripps.edu Thu Aug 10 08:18:07 1995 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.10/930601.1506) id IAA24819; Thu, 10 Aug 1995 08:13:51 -0400 Received: from aries.scripps.edu by scripps.edu (5.61/1.34) id AA06357; Thu, 10 Aug 95 05:13:48 -0700 Received: by aries.Scripps.EDU (4.1/SMI-4.1) id AA20288; Thu, 10 Aug 95 05:13:40 PDT Date: Thu, 10 Aug 95 05:13:40 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9508101213.AA20288@aries.Scripps.EDU> To: chemistry@ccl.net Subject: mopac93R2 compiling response summary Hi Folks, Below is a summary of responses to the MOPAC93 Release 2 question I posted yesterday. *************** The question again: I was wondering if anyone has been successful in compiling, linking, and running MOPAC93R2 on SGI workstations. With the help of some other folks (thanks!) I have been able to compile and link the program. However, when I run the program (for ethylene for example), instead of getting numbers for heats of fomration, etc., I get "nan". *************Summary of responses: I received sevenral responses including a makefile and offers to help me debug mine (thanks!). Several folks also suggested I check to make sure I am compiling with the -static option. The -static option turned out to be the key. Turns out that I had a few subroutines not being compiled with the option which caused the difficulties. Thanks to the CCL and in particular Ken Fountain Jon Erickson John M. McKelvey Georg Ostertag William A. Wylie Ralph J. Wolf Victor M. Rosas Garcia Luke Anthony Burke Dr. Satyam Priyadarshy Thanks again and With best regards, Rick Ross From sschulz@chemie.fu-berlin.de Thu Aug 10 11:26:25 1995 Received: from weasel.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/930601.1506) id LAA02350; Thu, 10 Aug 1995 11:12:03 -0400 Message-Id: <199508101512.LAA02350@www.ccl.net> Received: by weasel.chemie.fu-berlin.de (1.37.109.16/16.2) id AA290877470; Thu, 10 Aug 1995 17:11:10 +0200 From: Stefan Schulz Subject: ECP in GAMESS-US & GAUSSIAN92 To: chemistry@ccl.net Date: Thu, 10 Aug 95 17:11:10 MESZ X-Hpvue$Revision: 1.8 $ Mime-Version: 1.0 Content-Type: Message/rfc822 X-Vue-Mime-Level: 4 Mailer: Elm [revision: 70.85] Hi CCLers, I am currently using some general effective core potentials for sodium and nitrogen with the program GAMESS-US. The input I use to describe them within GAMESS-US is as follows $ECP Na-ECP GEN 2 1 3 -1.361911 1 76.2365 -1.715443 2 22.5231 -0.000102 2 1.6068 5 1.877655 0 1.5008 3.140947 1 8.2166 -32.322246 2 3.9471 31.911208 2 3.0990 -14.538661 2 2.4783 N-ECP GEN 2 1 3 -1.456021 1 73.0888 -4.872023 2 25.3408 -0.670937 2 7.4794 4 3.273330 0 2.3860 -9.608747 1 8.1610 69.864206 2 4.7425 -60.381084 2 4.1726 H-ECP NONE H-ECP NONE H-ECP NONE $END which apparently works quite fine. My problem is that now I want to use the same effective core potentials with GAUSSIAN92 and have used the following input: 7 7 9 9 9 Na-ECP 1 2 3 1 76.2365 -1.361911 2 22.5231 -1.715443 2 1.6068 -0.000102 5 0 1.5008 1.877655 1 8.2166 3.140947 2 3.9471 -32.322246 2 3.0990 31.911208 2 2.4783 -14.538661 N-ECP 1 2 3 1 73.0888 -1.456021 2 25.3408 -4.872023 2 7.4794 -0.670937 4 0 2.3860 3.273330 1 8.1610 -9.608747 2 4.7425 69.864206 2 4.1726 -60.381084 Does anybody out there have an idea if these two inputs really describe the same thing? There must be some difference since I get different results using these inputs ! (Since I also use a general basis set including D functions I have of course used the keyword 6d ) Having already checked the rest of my input file for consistency everything seems to be right. Could it be that one program does include the R^2 Jacobian factor into the power of R and the other does not ? Is there perhaps a tool to facilitate the migration of input files from GAMESS-US to GAUSSIAN92 and back ? Any help will be greatly appreciated ! Thanks PS Sorry for the somewhat lengthy problem description. Regards Stefan Schulz -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | Stefan Schulz | | sschulz@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5384 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Jeffrey.Gosper@brunel.ac.uk Thu Aug 10 11:56:33 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/930601.1506) id LAA03155; Thu, 10 Aug 1995 11:42:37 -0400 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <05861-0@monge.brunel.ac.uk>; Thu, 10 Aug 1995 16:42:08 +0100 Date: Thu, 10 Aug 1995 16:42:03 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: MOPAC reaction path calculations To: chemistry@ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I am trying to locate computational studies that make use of the reaction path calculation offered by MOPAC (i.e. use of the -1 optimization flag). I would therefore appreciate any pointers to published work on this matter. I'll summarize any responses as usual. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From masayuki@hsc.usc.edu Thu Aug 10 14:56:29 1995 Received: from hsc.usc.edu for masayuki@hsc.usc.edu by www.ccl.net (8.6.10/930601.1506) id OAA07222; Thu, 10 Aug 1995 14:53:19 -0400 Received: (masayuki@localhost) by hsc.usc.edu (8.6.12/8.6.4) id LAA09512 for chemistry@ccl.net; Thu, 10 Aug 1995 11:53:18 -0700 Date: Thu, 10 Aug 95 11:53:17 PDT From: Masayuki Yuki To: chemistry@ccl.net Subject: Summary:New Version of MOPAC Message-ID: Dear CCL Subscribers, My question was the following: I use MOPAC 6.0 for parametrization and partial charge calculation of molecules whose parameters are not available in AMBER 4.0 force field. Is there a later version of MOPAC? If there is, what is the difference from MOPAC 6.0? Does it result in improved parametrization? Is it worth getting it? Is there an ftp site from which I can get it? Thank you for everyone who has responded to my question. In summary, the new versions of MOPAC are MOPAC7, MOPAC93, and AMPAC 5.0. MOPAC 7 and MOPAC93 yield the same result as MOPAC6. MOPAC93 is available from QCPE for $150. AMPAC 5.0 is available from Semichem, Inc. Dr. Roberto Rivelino de M Moreno, here is the summary of the responses. Dear Masayuki, you wrote: > >I use MOPAC 6.0 for parametrization and partial charge calculation of >molecules whose parameters are not available in AMBER 4.0 force field. Is >there a later version of MOPAC? If there is, what is the difference from >MOPAC 6.0? Does it result in improved parametrization? Is it worth getting >it? Is there an ftp site from which I can get it? Yes, there is a newer version: MOPAC7 (for developers) and MOPAC93 (for production work), both are more or less the same. The main difference between version 6 and 93 are some added functionality like a solvent model, and some improved optimization routines. I haven't seen any significant speed-up of the calculations, however, the EF optimization seems to be a real improvement. No, the results would be the same for your parametrization and you have to decide for yourself whether to get or not. Many tools are for MOPAC6 output and therefore have to be rewritten for the slightly different MOPAC93 results (or the output of version 93 has to be modified). MOPAC93 is available from QCPE at their normal cost (about 150 US$). MOPAC7 is in the archive of this list (http://www.ccl.net/ccl/cca.html). Hope this helps, Cheers! Rainer. Rainer Koch Department of Chemistry University of Queensland Brisbane, Queensland 4072 koch@chem.chemistry.uq.oz.au > : Hello Masayuki > : > : Could I share with you all replies you could receive ? > : Thank you in advance. > : > : Roberto Rivelino de M. Moreno > : Instituto de Quimica > : Universidade Federal da Bahia - Brasil > : e-mail: rivelino@ufba.br The version recommended for academic use is MOPAC 93, available from QCPE. It has no, or few, new parameters, but runs much faster and is more robust than MOPAC 6. Jimmy Stewart Dear Dr. Yuki, In reply to: > Is there a later version of MOPAC? If there is, what is the > difference from MOPAC 6.0? There is indeed a more recent version of MOPAC available, version 7.0. I would like to suggest to you AMPAC 5.0 with Graphical User Interface as an excellent alternative to MOPAC. My company sells and supports AMPAC, which is a much advanced version of the old MOPAC and is front-ended by an excellent graphics interface. There are also new parameterizations in AMPAC that are not present even in the newest versions of MOPAC. I would be happy to forward you additional information if you would provide me with your regular mail address. Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From jkl@ccl.net Thu Aug 10 21:08:59 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id VAA12064; Thu, 10 Aug 1995 21:03:43 -0400 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.6.10/930601.1506) id VAA16164; Thu, 10 Aug 1995 21:03:40 -0400 From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id VAA00625; Thu, 10 Aug 1995 21:03:39 -0400 Date: Thu, 10 Aug 1995 21:03:39 -0400 Message-Id: <199508110103.VAA00625@krakow.ccl.net> To: chemistry@ccl.net Subject: this is a test Cc: jkl@ccl.net This is a test of chemistry -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From jkl@ccl.net Thu Aug 10 21:55:57 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id VAA12987; Thu, 10 Aug 1995 21:54:07 -0400 Received: from aqua.chem.nagoya-u.ac.jp for mito@aqua.chem.nagoya-u.ac.jp by bedrock.ccl.net (8.6.10/930601.1506) id VAA16888; Thu, 10 Aug 1995 21:54:04 -0400 Received: (from mito@localhost) by aqua.chem.nagoya-u.ac.jp (8.6.9+2.4W/3.3Wb-94112516) id KAA02582; Fri, 11 Aug 1995 10:49:47 +0900 Date: Fri, 11 Aug 1995 10:49:47 +0900 From: Masakatsu Ito Message-Id: <199508110149.KAA02582@aqua.chem.nagoya-u.ac.jp> To: chemistry@ccl.net CC: kando@postman.riken.go.jp Subject: Summary: The photoproduction of cis,trans-C8H10 ... Hello Netters, I have recently posted a question about the photo- isomerization yield of all trans-octatetraene and the ratio of cis,trans-isomer to all trans-one. Barry R Smith have told me the very useful literature. I'm very gratefull to him. He recommended: 1."Octatetraene Photoisomerization",Bryan E. Kohler, Chem. Rev. 1993, 93, 41-54 And it contains other useful references. 2."cis-trans photoisomerization of 1,3,5,7-octatetraene in n-hexane at 4.2K", M.F.Grandville,G.R.Holtom, and B.E.Kohler, Proc.Natl.Acad.Sci.USA,77,31-33(1980) 3."Radiationless decay of 1,3,5,7-octatetraene",J.R.Ackerman and B.E.Kohler,J.Chem.Phys.,77,3967(1982) 4."Double-bond isomerization barrier in the 2Ag excited singlet state of cis,trans-1,3,5,7-octatetraene",J.R.Ackerman and B.E.Kohler,J.Am.Chem.Soc.,106,3681(1984) 5."Barriers in the excited 2Ag state for the cis,trans isomerization of cis,cis-octatetrane: General features of the excited state potentical",B.E.Kohler,P.Mitra, and P.West,J.Chem.Phys.,85,4436 (1986) 6."Photochemical hole burning for 1,3,5,7-octatetrane in n-hexane", G.Adamson,G.Gradl, and B.E.Kohler, J.Chem.Phys.,90,3038(1989) So far I cannot find the information about the photoismorization yield. But I've got other interesting information from these references. Thanks. Masakatsu Ito Department of Structual Molecular Science The Graduate University for Advanced Studies Tel 81(Japan)-52-789-3656 Fax 81(Japan)-52-789-3551 E-mail mito@aqua.chem.nagoya-u.ac.jp >From: barry@chem3.ch.kcl.ac.uk (Barry R Smith ) >Message-Id: <9508021002.AA21467@chem3.ch.kcl.ac.uk> >To: mito@aqua.chem.nagoya-u.ac.jp >Subject: octatetraene photoisomerization > >Try looking at a recent review article titled >"Octatetraene Photoisomerization" by Bryan E. Kohler >(Chem. Rev. 1993, 93, 41-54). I'm not sure if it >says much about the yields, but is a good place to >start + contains lots of other references. > >Barry R. Smith, Dept. of Chemistry, King's College London, UK.