From MKRISM@tifrvax.tifr.res.in Wed Jan 26 00:44:28 1994 Received: from tifrvax.tifr.res.in for MKRISM@tifrvax.tifr.res.in by www.ccl.net (8.6.4/930601.1506) id AAA12645; Wed, 26 Jan 1994 00:24:28 -0500 From: Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01H84897DVLC000BG4@tifrvax.tifr.res.in>; Tue, 25 Jan 1994 23:19 +0530 Date: Tue, 25 Jan 1994 23:19 +0530 Subject: franck-factors for ammonia To: Chemistry@ccl.net Message-id: <01H84897DVLC000BG4@tifrvax.tifr.res.in> X-VMS-To: IN%"Chemistry@ccl.net" Dear Friends, I am looking for the franck-condon factors for the excitation of ammonia from the ground electronic state to the different excited states. I would like to know if there is any compilation of the franck-condon factors for the excitations, in case of other small molecules like water,H2S etc., also. I would be grateful to recieve any references which have this information available. Thanking you in advance. M.Krishnamurthy, Atomic and Molecular Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Navy Nagar, Bombay 400 005. India. E-mail: MKRISM@tifrvax.tifr.res.in From koyanagi@watsci.uwaterloo.ca Wed Jan 26 01:44:32 1994 Received: from watserv1.uwaterloo.ca for koyanagi@watsci.uwaterloo.ca by www.ccl.net (8.6.4/930601.1506) id AAA12788; Wed, 26 Jan 1994 00:49:52 -0500 Received: from watsci.uwaterloo.ca by watserv1.uwaterloo.ca with SMTP id ; Wed, 26 Jan 94 00:49:48 -0500 Received: by watsci.uwaterloo.ca (931110.SGI/931108.SGI.ANONFTP) for @watserv1.uwaterloo.ca:CHEMISTRY@ccl.net id AA20198; Wed, 26 Jan 94 00:49:40 -0500 From: koyanagi@watsci.uwaterloo.ca (Greg Koyanagi) Message-Id: <9401260549.AA20198@watsci.uwaterloo.ca> Subject: Gaussian-92 difficulty... X RAN OUT IN RYSROT To: CHEMISTRY@ccl.net Date: Wed, 26 Jan 94 0:49:39 EST X-Mailer: ELM [version 2.3 PL11] Dear Comp-Chem netters: I've sent the following letter to Gaussian asking for assistance, however we do not subscribe to their "On-demand-help-line" so any response I recieve may not arrive in a timely manner, if at all. I would appreciate any info or solutions from someone in-the-know or who has had and conquered a similar problem. Thanks in advance for any and all help, Greg Koyanagi E-mail (koyanagi@watsci.uwaterloo.ca) Department of Chemistry Voice 519-885-1211 (x6388) University of Waterloo FAX 519-746-0453 Waterloo, Ontario, CANADA N2L 3G1 Text of letter: ************************************************************************ I have been attempting to perform frozen-core MP2 frequency calculations on small hydrocarbon neutrals and cations and have had difficulty in persuading the computations to complete. The computer being used is an SGI with (8x)-33MHz R3000 chips, revision 2. There are 128 MBytes of main memory and 5GB of scratch disk space. The version of gaussian gives: *************************************** Gaussian 92: SGI-G92RevE.2 4-Aug-1993 22-Oct-1993 *************************************** Several systems have resulted in the computation dying with the error: ===================================================================== Use MO integrals over full window. 2PDM will be sorted in 1 passes. Compute integral second derivatives. ... and contract with generalized density number 2. Use density number 2. RysSet: KIntrp= 2354 KCalc= 0 KAssym= 2821 Use density number 2. Adding in external 2PDM contributions. TWLHES: FMTGEN WAS CALLED 42612 TIMES. Compute integral second derivatives. DF integral derivatives using scalar Rys method. Use density number 2. Adding in external 2PDM contributions. Standard cutoffs used. PQCut1= 1.00D-20 PQCut2= 1.00D-20 PQCut3= 1.00D+02 PQCut4= 1.00D-20 X RAN OUT IN RYSROT. Error termination in Lnk1e. sh: 9799 Memory fault - core dumped Which was produced from the input file: ====================================== %Chk=ch2oh02 %NProc=1 %Mem=2800000 #N MP2/6-31+G(2d,2p) GEOM=CHECK GUESS=CHECK FREQ TEST ch2oh(+) freq 1 1 ====================================== The checkpoint file was produced by the following input file: ============================================================ %Chk=ch2oh02 #N MP2/6-31+G(2d,2p) OPT=TIGHT TEST ch2oh(+) 1 1 C O C rCO H1 C rCH1 O HCO1 H2 C rCH2 O HCO2 H1 HCOH H3 O rOH3 C HOC3 H1 HOCH rCO 1.252489 rCH1 1.087204 rCH2 1.085003 rOH3 0.981446 HCO1 121.477 HCO2 115.408 HOC3 114.484 HCOH 180.0 HOCH 0.0 ============================================================ Which completed and ended with: ==================================================== Test job not archived. 1\1\UNIVERSITY OF WATERLOO-WATSCI\FOPT\RMP2-FC\6-31+G(2D,2P)\C1H3O1(1+ )\KOYANAGI\22-Oct-1993\1\\#N MP2/6-31+G(2D,2P) OPT=TIGHT TEST\\ch2oh(+ )\\1,1\C\O,1,rCO\H,1,rCH1,2,HCO1\H,1,rCH2,2,HCO2,3,HCOH,0\H,2,rOH3,1,H OC3,3,HOCH,0\\rCO=1.252489\rCH1=1.087204\rCH2=1.085003\rOH3=0.981446\H CO1=121.477\HCO2=115.408\HOC3=114.484\HCOH=180.\HOCH=0.\\Version=SGI-G 92RevE.2\State=1-A'\HF=-114.1741398\MP2=-114.5061648\RMSD=2.208e-09\RM SF=1.082e-06\Dipole=0.6354071,0.,-0.5293646\PG=CS [SG(C1H3O1)]\\@ ==================================================== I have determined that the link executing was calling a utility in utilnz.F which has the documenting comments: COPYRIGHTED STUFF DELETED FOR PUBLIC MAILING.... * * Insert here comments for a subroutine that attempts to * determine roots of an equation involved in the * Rys method. SUBROUTINE RYSROT * Subsequently, I have successfully computed the frequencies in the above instance using freq=numer, however, this would prove too large a task for some of the systems I wish to study. (My best estimate for the next largest is 16-20 days and 60-100 days for the system above that). Similar analytic computations have completed in 3 to 4 days. I would appreciate any ideas or information you may have that would allow me to compute the frequencies using the analytic algorithm. Sincerly, Greg Koyanagi E-mail (koyanagi@watsci.uwaterloo.ca) Department of Chemistry Voice 519-885-1211 (x6388) University of Waterloo FAX 519-746-0453 Waterloo, Ontario, CANADA N2L 3G1 From jkshin@radon.sait.samsung.co.kr Wed Jan 26 02:44:36 1994 Received: from han.hana.nm.kr for jkshin@radon.sait.samsung.co.kr by www.ccl.net (8.6.4/930601.1506) id BAA13777; Wed, 26 Jan 1994 01:54:15 -0500 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA19624; Wed, 26 Jan 94 15:55:51 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA26000; Wed, 26 Jan 94 15:55:23 KST Received: by radon.sait.samsung.co.kr (920330.SGI/920502.SGI.AUTO) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA02334; Wed, 26 Jan 94 15:56:29 +0900 Date: Wed, 26 Jan 94 15:56:29 +0900 From: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9401260656.AA02334@radon.sait.samsung.co.kr> To: chemistry@ccl.net Subject: Journal Information Dear Netters: I would like to know about the journal "Theo. Chim. Acta". Does anyon know the name and address of the editor in chief and how much time it takes(in average) to get reply after submission of manuscripts? Any kinds of information will be greatly appreciated. Thanks in advance. Jai K. Shin: jkshin@radon.sait.samsung.co.kr From dirk@rulglj.LeidenUniv.nl Wed Jan 26 05:44:32 1994 Received: from rulway.LeidenUniv.nl for dirk@rulglj.LeidenUniv.nl by www.ccl.net (8.6.4/930601.1506) id EAA14717; Wed, 26 Jan 1994 04:56:59 -0500 Received: from rulglj.LeidenUniv.nl by rulway.LeidenUniv.nl with SMTP id AA06318 (5.65c+/IDA-1.4.4 for <@RULWAY.LEIDENUNIV.NL:CHEMISTRY@ccl.net>); Wed, 26 Jan 1994 10:56:37 +0100 Received: by rulglj.LeidenUniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:CHEMISTRY@ccl.net id AA00811; Wed, 26 Jan 94 10:57:44 -0800 Date: Wed, 26 Jan 94 10:57:44 -0800 From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) Message-Id: <9401261857.AA00811@rulglj.LeidenUniv.nl> To: CHEMISTRY@ccl.net Subject: Fitting molecular structures Hello all, I have two sets of cartesian coordinates. They both contain a common part, say a five membered ring. The orientation of each molecule is different. I want both molecules to have the same orientation based on the common part. Does anyone of you out there tried to solve this ? Any help will be appreciated. ------------------------------------------------------------------------------ Dirk Huckriede Conformational Analysis Group Gorlaeus Laboratories Leiden University P.O. Box 9502 Phone : +31 71 274505 2300 RA Leiden Fax : +31 71 274488 The Netherlands E-mail : dirk@rulglj.leidenuniv.nl ------------------------------------------------------------------------------ "to be or nut^H^H^H -- sh^Gt, how do I delete..^?^?^? Oh No Oh NO^D^D^D -- How do I get out of this thing anyway^C^C^C Kill it^Z^Z^Z (mumble mumble) Bus error (core dumped) ------------------------------------------------------------------------------ From tgocsv@urc.tue.nl Wed Jan 26 07:44:34 1994 Received: from mailhost.tue.nl for tgocsv@urc.tue.nl by www.ccl.net (8.6.4/930601.1506) id HAA15406; Wed, 26 Jan 1994 07:40:05 -0500 From: Received: from alliant.urc.tue.nl by mailhost.tue.nl with SMTP id AA24172 (5.65c/IDA-1.4.4 for ); Wed, 26 Jan 1994 13:39:38 +0100 Received: by alliant.urc.tue.nl (5.0/1.51) id AA24253; Wed, 26 Jan 94 13:41:59 EST Message-Id: <9401261241.AA24253@alliant.urc.tue.nl> Subject: Fitting of CD spectra To: CHEMISTRY@ccl.net Date: Wed, 26 Jan 94 13:41:58 EST X-Mailer: ELM [version 2.3 PL6] Dear Netters, Does anybody have experience with program(s) to fit CD spectra and programs which can do CD deconvolution? Thanks already. Michiel Bouman From b_duke@lacebark.ntu.edu.au Wed Jan 26 07:58:28 1994 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.4/930601.1506) id GAA15301; Wed, 26 Jan 1994 06:54:07 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA07816; Wed, 26 Jan 1994 21:22:17 -0600 Message-Id: <9401270322.AA07816@lacebark.ntu.edu.au> Subject: xmol for IBM RISC 6000? To: CHEMISTRY@ccl.net (chemistry) Date: Wed, 26 Jan 1994 21:22:13 -0600 (CST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 671 G'day again, CCL Netters, xmol sounds a really useful program and there is stuff in the CCL archives that prepares data for it - xvibs and some perl scripts >from Jan. However I gather it runs only on SGI. Does anyone have any news about a port to the RS6K? I know some progress has been made in Leo Radom's group in Canberra by Tony Scott, but it is not complete. Is anyone else working on this? Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From b_duke@lacebark.ntu.edu.au Wed Jan 26 07:59:08 1994 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.4/930601.1506) id GAA15278; Wed, 26 Jan 1994 06:46:32 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA10367; Wed, 26 Jan 1994 21:14:45 -0600 Message-Id: <9401270314.AA10367@lacebark.ntu.edu.au> Subject: chelpg and g92. To: CHEMISTRY@ccl.net (chemistry) Date: Wed, 26 Jan 1994 21:14:30 -0600 (CST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1022 G'day, CCL Netters, The version of chelpgunix.f in the CCL archives reads G90 chk files. Does anyone have a version that reads G92 files? It would be necessary (I think) to alter COMMON /MOL/ since MaxAtm in G90 was 400 and it is 1000 in G92. Changes would also need to be made in COMMON /B/. I also suspect that reading G92 files would come across the same problem I asked about recently reading C in /MOL/ in psig90. This gives incorrect results in some cases. It seems necessary to read and then untangle the coordinates of each shell. Alternately, chelpg could be written to read the ascii chk file produced using formchk. If anyone does have a version for g92, could it be put in the CCL archives? It would save us reinventing the wheel. Cheers, Brian -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From young@slater.cem.msu.edu Wed Jan 26 08:44:43 1994 Received: from msu.edu for young@slater.cem.msu.edu by www.ccl.net (8.6.4/930601.1506) id IAA15729; Wed, 26 Jan 1994 08:09:59 -0500 Received: from slater.cem.msu.edu by msu.edu (IBM VM SMTP V2R2) with TCP; Wed, 26 Jan 94 08:10:08 EST Received: by slater.cem.msu.edu (920330.SGI/911001.SGI) for @msu.edu:chemistry@ccl.net id AA14778; Wed, 26 Jan 94 08:10:45 -0500 Date: Wed, 26 Jan 94 08:10:45 -0500 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9401261310.AA14778@slater.cem.msu.edu> To: chemistry@ccl.net Subject: Gaussian quirks Hi, I'm sure many of the subscribers to this list are fluent users of the Gaussian XX programs. Although these are wonderful programs, the number of revsions and authors has created a number of places where the manual is either wrong or too vague. I don't mean to offend the authors. I couldn't keep on top of that volume of code either. However, my question is this does anyone have a compilation of the various work arounds for these quirks? Following are two that I have found. 1. In order to request a tighter convergence criteria, the command "conv=7" for 10**-7 convergence doesn't work in our version, but the command "iop(5/6=7)" will have the same result. 2. When doing a CISD calculation, the command "pop=no" does not give a complete set of natural orbitals with occupation numbers. (By complete set, I desire all orbitals with non-zero occupations.) However, if you are creating a cube file from a CI calculation and have the commands "pop=no density=ci cubedensity=density" THEN you get the natural orbitals. Please send comments directly to me young@slater.cem.msu.edu and I will summarize for the list. Dave Young young@slater.cem.msu.edu youngdc@msucem From desmarai@CHIMCN.UMontreal.CA Wed Jan 26 09:44:35 1994 Received: from condor.CC.UMontreal.CA for desmarai@CHIMCN.UMontreal.CA by www.ccl.net (8.6.4/930601.1506) id JAA16283; Wed, 26 Jan 1994 09:18:39 -0500 Received: from chims1.CHIMCN.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA18756 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 26 Jan 1994 09:16:23 -0500 Received: by chims1.CHIMCN.UMontreal.CA (930416.SGI/5.17) id AA13513; Wed, 26 Jan 94 09:16:24 -0500 From: desmarai@CHIMCN.UMontreal.CA (Desmarais Normand) Message-Id: <9401261416.AA13513@chims1.CHIMCN.UMontreal.CA> Subject: For user of SURVIB & POLYMODE ONLY!!! To: chemistry@ccl.net (Computer Chemistry List) Date: Wed, 26 Jan 1994 09:16:23 -0500 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1025 Hello! a friend of me needs some information about SURVIB and POLYMODE... He's french and his english is very bad so if you can write in french do it please... Here is the problem: SURVIB ====== He wants to calculate the IR intensities of the overtone and hot bands (in french: les bandes harmoniques et les bandes de combinaisons). He need to know if he must give: 1) the dipole moment, 2) the component of the dipole moment in the symetry axis, 3) the component of the dipole moment in the plane of symetry if there is one? POLYMODE ======== He wants to know how to calculate the energy of a giving state... Must he calculates it from the energy of the state (000..0) of the first SCF-CI iteration or must he recalculates it for each (000..0) states of the diferent iterations? I hope the questions are clear enough... if you need more input just send me a message. Please send your answer to me, not to the CCL. Thank you for your concern! Normand Desmarais. desmarai@chims1.chimcn.umontreal.ca From raman@bioc01.uthscsa.edu Wed Jan 26 09:46:18 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id JAA16252; Wed, 26 Jan 1994 09:13:37 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 26 Jan 1994 8:14:23 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA08688; Wed, 26 Jan 94 08:13:56 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9401261413.AA08688@bioc01.uthscsa.edu> Subject: Re: Fitting of CD spectra To: tgocsv@urc.tue.nl Date: Wed, 26 Jan 1994 08:13:55 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9401261241.AA24253@alliant.urc.tue.nl> from "tgocsv@urc.tue.nl" at Jan 26, 94 01:41:58 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1286 > Does anybody have experience with program(s) to fit CD spectra > and programs which can do CD deconvolution? Thanks already. Yes, I do that quite often for Proteins. There are different algorithms for accomplishing this and the most popular of which is called VARSELEC >from Curtis Johnson's group (utilises SVD). Gerald Fasman also distributes code to deconvolve CD spectra. Of course, the most rigorous one I know of is called CONTIN (by Provencher). I would be more than happy to answer any specific questions. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From walt@ibm1.carb.nist.gov Wed Jan 26 09:47:02 1994 Received: from ENH.NIST.GOV for walt@ibm1.carb.nist.gov by www.ccl.net (8.6.4/930601.1506) id IAA16118; Wed, 26 Jan 1994 08:56:28 -0500 Received: from ibm1.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01H84SETQCR4000TNV@ENH.NIST.GOV>; Wed, 26 Jan 1994 08:56:16 EDT Received: by ibm1.carb.nist.gov (AIX 3.2/UCB 5.64/4.03) id AA17996; Wed, 26 Jan 1994 08:56:43 -0500 Date: Wed, 26 Jan 1994 08:33:28 -0500 (EST) From: "Dr. Walter J. Stevens" Subject: Background Priority To: Chemistry List Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Some time ago I posted a question to the list about executing jobs in the background on SGI and IBM workstations. I was interested in execution priorities that would allow a job to soak-up unused machine cycles without interfering with foreground or higher priority jobs. The 'nice' command doesn't have enough range. Thanks to everyone who responded. We haven't made much progress with with IBM AIX. Here is a summary of the responses: - Use 'npri' on the SGI workstations. eg. npri -h 150 This works pretty well, but I haven't found an equivalent command for IBM AIX. - Use NQS (Network Queuing System) to distribute load and the 'qdel -s' option to stop jobs during the day. This is not quite what we're looking for, since interactive and priority foreground use continue at all hours. - IBM RS/6000s do not timeshare well. This is true. We usually run two jobs max. However, a 'sponge' priority for deep background execution isn't really timesharing. - Try 'Batch 4.0' for SGI which is available from Scott Presnell. Contact him at srp@zgi.com. Free for academics and gov. but need license. Docs and man pages available (FTP 128.218.21.42). We haven't tried this yet, but it does have provisions for giving high priority to active console users. Looks interesting. - Try the commercial package 'nanny' from Terry Coley (terry@wag.caltech.edu). This is an automatic priority controller that can give priority to active console users and can also balance the percentage of cycles given to each user. A free trial version is available at ftp.wag.caltech.edu:/pub/nanny. We are evaluating this one. No conclusions so far. -------------------------------------------------- Dr. Walter J. Stevens Center for Advanced Research in Biotechnology National Institute of Standards and Technology and University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Phone: (301) 738-6264 FAX : (301) 738-6255 E-MAIL: walt@ibm1.carb.nist.gov -------------------------------------------------- From rsjuds@california.sandia.gov Wed Jan 26 12:44:58 1994 Received: from california.sandia.gov for rsjuds@california.sandia.gov by www.ccl.net (8.6.4/930601.1506) id MAA18396; Wed, 26 Jan 1994 12:25:30 -0500 Received: from localhost by california.sandia.gov (8.6.4/1.15) id JAA29153; Wed, 26 Jan 1994 09:25:24 -0800 Date: Wed, 26 Jan 1994 09:25:24 -0800 From: rsjuds@california.sandia.gov (judson richard s) Message-Id: <199401261725.JAA29153@california.sandia.gov> To: chemistry@ccl.net Subject: atom type conversions Cc: rsjuds@california.sandia.gov Folks, Does anyone out there have routines that do a reasonable conversion between atom types in different MM force fields. I'm particularly interested in baing able to take files that Sybyl puts out and convert them to something that CHARMm can read. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering/8117 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | email: rsjuds@ca.sandia.gov | | | ----------------------------------------------- From m10!frisch@uunet.UU.NET Wed Jan 26 12:56:15 1994 Received: from relay2.UU.NET for m10!frisch@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id MAA18365; Wed, 26 Jan 1994 12:20:49 -0500 Received: from spool.uu.net (via LOCALHOST) by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwant15010; Wed, 26 Jan 94 12:18:47 -0500 Message-Id: <9401261718.AAwant15010@relay2.UU.NET> Received: from m10.UUCP by uucp6.uu.net with UUCP/RMAIL (queueing-rmail) id 115332.17377; Wed, 26 Jan 1994 11:53:32 EST Received: by m10.gaussian.com; Wed, 26 Jan 94 11:50:25 EST Date: Wed, 26 Jan 94 11:50:25 EST From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: chelpg and g92. To: chemistry@ccl.net In-Reply-To: , Wed, 26 Jan 1994 21:14:30 -0600 (CST) Brian Salter-Duke asked: G'day, CCL Netters, The version of chelpgunix.f in the CCL archives reads G90 chk files. Does anyone have a version that reads G92 files? It would be necessary (I think) to alter COMMON /MOL/ since MaxAtm in G90 was 400 and it is 1000 in G92. Changes would also need to be made in COMMON /B/. I also suspect that reading G92 files would come across the same problem I asked about recently reading C in /MOL/ in psig90. This gives incorrect results in some cases. It seems necessary to read and then untangle the coordinates of each shell. Alternately, chelpg could be written to read the ascii chk file produced using formchk. If anyone does have a version for g92, could it be put in the CCL archives? It would save us reinventing the wheel. Gaussian 92 can do potential-derived charges itself -- Pop=ChelpG on the route card will do it. The default atomic radii used are those recommended by Breneman, but you can specific your own if you like. Mike Frisch ------- From YQIN@aardvark.ucs.uoknor.edu Wed Jan 26 12:56:55 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id MAA18207; Wed, 26 Jan 1994 12:00:49 -0500 From: Message-Id: <199401261700.MAA18207@www.ccl.net> Date: Wed, 26 Jan 94 10:58 CST Subject: Where can I get the frequency of phenoxide and phenol cation? To: CHEMISTRY@ccl.net, MAILSERV@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net",IN%"MAILSERV@ccl.net","chemistry-request@ccl.net",IN%"chemistry-search@ccl.net" Dear netters: I am looking for both experiment and theoritical works on the vibrational frequency measurement (or calculation), and spin density measurement (for phenol cation only) of the phenoxide anion and phenol cation. I did some literature search, I do get two papers ( J. Chem Phys. 82, 5329 1985 by S. Anderson and co-workers; Int. J. Mass Spec. and Ion Process 117,601,1992 by R. F. Gunion and co-workers). I would appreciate it very much if someone can provide more information. Thank you very much in advance. Yuli qin yqin@aardvark.ucs.uoknor.edu From tudor@wucmd.wustl.edu Wed Jan 26 13:45:01 1994 Received: from wugate.wustl.edu for tudor@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id NAA19045; Wed, 26 Jan 1994 13:14:30 -0500 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA17641; Wed, 26 Jan 1994 12:14:24 -0600 Received: by wucmd (911016.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA01383; Wed, 26 Jan 94 16:53:09 GMT Date: Wed, 26 Jan 1994 10:38:27 -0600 (CST) From: Tudor Oprea Subject: Re: Fitting molecular structures To: Dirk Huckriede Cc: CHEMISTRY@ccl.net In-Reply-To: <9401261857.AA00811@rulglj.LeidenUniv.nl> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 26 Jan 1994, Dirk Huckriede wrote: > > Hello all, > > I have two sets of cartesian coordinates. They both contain a common part, say > a five membered ring. The orientation of each molecule is different. > I want both molecules to have the same orientation based on the common part. > Does anyone of you out there tried to solve this ? > > Any help will be appreciated. > > ------------------------------------------------------------------------------ > Dirk Huckriede > > Conformational Analysis Group > Gorlaeus Laboratories > Leiden University > > P.O. Box 9502 Phone : +31 71 274505 > 2300 RA Leiden Fax : +31 71 274488 > The Netherlands E-mail : dirk@rulglj.leidenuniv.nl > ------------------------------------------------------------------------------ > "to be or nut^H^H^H -- sh^Gt, how do I delete..^?^?^? Oh No Oh NO^D^D^D -- How > do I get out of this thing anyway^C^C^C Kill it^Z^Z^Z (mumble mumble) > Bus error (core dumped) > ------------------------------------------------------------------------------ First put this line in your .cshrc - it will help you get OUT limit coredumpsize 0 kbytes ;-) Second, it depends on the type of investigation you are doing. If a geometric fit satisfies you, just match the atoms you think correspond (any modeling program will do that). If you have a pharmacophore hypothesis, try to fit the common pharmaco- phoric elements, regardless of the actual structural fit. This should give you an idea of how the two structures fit in the same binding site. If you can go sophisticated, use the field-fit procedure in Sybyl, that would allow you to fit one ligand in the steric and electrostatic (or in either one of them) individually. I advise you relax the resulting field-fitted structure using steepest-descent for ~100 steps, then conjugate gradient (to go to the nearest pit). Clark et al, Tetrahedron Comput Methodol 1990 3:47 for field fit It is possible to use the approach of Perkins & Dean (JCAMD 1993 7:155) which will allow you to use simulated annealing & cluster analysis to get the best match. RECEPTOR & Constrained systematic search are available in Sybyl - use that in conjunction with the Active Analog Approach Dammkoehler et al, JCAMD 1989 3:3 If you want to go automatic, use DISCO (from Yvonne Martin, Abbott) see Trends in Molecular Modelling '92 (ESCOM, Leiden - your town! 1993), ed. CG Wermuth, for Martin et al, pp 20 - and references therein. Other procedures that you may use are: Grid (from Peter Goodford) and Cosmic (from Andy Vinter) - both probe the molecules with H+, HO- and H20 and superpose fields, rather than structures. Contact me if you have any questions... --Tudor ========================== Tudor-Ionel Oprea = Tel. (1-314) 935 4672 = Research Associate = Fax. (1-314) 935 4979 = Washington University Center for Molecular Design = Email: = Lopata 510, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = St.Louis MO 63130 ========================== From kcross@cas.org Wed Jan 26 14:44:41 1994 Received: from srv01s4.cas.org for kcross@cas.org by www.ccl.net (8.6.4/930601.1506) id OAA20006; Wed, 26 Jan 1994 14:07:38 -0500 Date: Wed, 26 Jan 94 14:07:05 EST From: kcross@cas.org (Kevin P. Cross Ext. 3192) Message-Id: <9401261407.AA6894@cas.org> Subject: Spring ACS Scientific Visualization and Multi-Media Program To: chemistry@ccl.net Below is the program for the Scientific Visualization and Multi-Media Symposium at the Spring ACS National Meeting in San Diego March 13-18th. Mark your calendars now and plan to stay through Thursday for an exciting time! Sincerely, James W. Cooper, jwcnmr@yktvmv.vnet.ibm.com Kevin P. Cross, kcross@cas.org Weige Xue, weigex@autodesk.com (the symposium organizers) ACS SPRING NATIONAL MEETING: COMPUTERS IN CHEMISTRY DIVISION PROGRAM FOR SCIENTIFIC VISUALIZATION AND MULTI-MEDIA SYMPOSIUM WEDNESDAY MORNING MARCH 16, 1994 8:45-8:55 Introductory Remarks 8:55-9:25 VISUALIZATION OF MULTIDIMENSIONAL NMR DATA, Robert D. Johnson, Peter Bluemler, Richter Rafey and Dominique Brodbeck, IBM Almaden Research Center 9:25-9:55 VISUALIZATION OF CHANGES ON ELECTRONIC PROPERTIES DURING CHEMICAL REACTIONS, James O. Currie, Jr., Pacific University 9:55-10:25 VISUALIZING MOLECULAR ELECTROSTATIC FIELDS, Richard Sefecka, David Silverman and Dan Platt, IBM T J Watson Research Center 10:25-10:30 break 10:30-11:00 VISUALIZING IR AND NMR SPECTROSCOPY, Charles B. Abrams, McGill University 11:00-11:30 COMPUTER GRAPHIC APPROACHES TO VISUALIZING BIOMOLECULAR INTERACTIONS, Arthur J. Olson, Molecular Graphics Laboratory, The Scripps Research Institute, 11:30-12:00 VISUALIZATION AND ANIMATION OF ORGANIC REACTIONS ON A PC. James W. Cooper and Bernard Landman, IBM Watson Research THURSDAY MORNING MARCH 17, 1994 9:00 - FACILITATING PROBLEM-SPECIFIC MOLECULAR VISUALIZATION: THE MIDASPLUS DELEGATE FACILITY, Conrad Huang, Eric Pettersen, Greg Couch, Thomas Ferrin, University of California, San Francisco. 9:30 - MOLECULAR MODELING AT THE METACENTER, Richard E. Gillilan, Cornell Theory Center. 10:00 - DEVELOPMENTS IN SCIENTIFIC VISUALIZATION AND MULTI-MEDIA, Mark E. Berger, Silicon Graphics. 10:30 - PROTEIN SURFACES AS TARGETS FOR STRUCTURE-BASED DRUG DESIGN, Brad A. Jameson, J. M. McDonnell, R. Wiaderkiewicz, Thomas Jefferson University. 11:00 - MAPPING CONFIGURATIONAL HYPERSPACE IN PROTEINS, Leo S. D. Caves, J. D. Evanseck, M. Karplus, Harvard University. 11:30 - ANIMATION OF CHEMICAL REACTIONS: NEW TOOLS FOR ASSIGNING MECHANISM, Warren J. Hehre, Wavefunction, Inc. THURSDAY AFTERNOON MARCH 17, 1994 1:00 - A TOOL TO ENHANCE THE COMMUNICATION OF COMPLEX BIOMEDICAL CONCEPTS, Rod Cuddihee, Peter B. Goncalves, Sacred Heart University. 1:30 - MULTIMEDIA AND SCIENTIFIC VISUALIZATION IN CHEMICAL EDUCATION, John W. Moore, Paul F. Schatz, University of Wisconsin-Madison. 2:00 - VISUALIZATION OF ORBITAL POLARIZATION USING AVS, Doug A. Smith, The University of Toledo. 2:30 - DEVELOPMENT OF COMPUTER GRAPHIC VISUALIZATION AIDS FOR THE UNDERGRADUATE CHEMISTRY CURRICULUM, Nathan S. Lewis, Juniko Moody, Christopher W. Bryant, Mark Huber, Scott Townsend, Michael Medaglia, Anthony Molinaro, Andre Yew, California Institute of Technology. 3:00 - VISUAL CRYSTALLOGRAPHY, Erin N. Thornton, Anthony C. Hess, Chance R. Younkin, Battelle Pacific Northwest Laboratory. 3:30 - ADVANCED VISUALIZATION TECHNIQUES FOR POLYMER FLOW MODELING, Pascal J. B. Landi, Hoechst Celanese Corp. From jamorskc@CHIMCN.UMontreal.CA Wed Jan 26 15:44:45 1994 Received: from condor.CC.UMontreal.CA for jamorskc@CHIMCN.UMontreal.CA by www.ccl.net (8.6.4/930601.1506) id PAA21206; Wed, 26 Jan 1994 15:33:00 -0500 Received: from chims1.CHIMCN.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA00031 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 26 Jan 1994 15:30:43 -0500 Received: by chims1.CHIMCN.UMontreal.CA (930416.SGI/5.17) id AA00671; Wed, 26 Jan 94 15:30:42 -0500 From: jamorskc@CHIMCN.UMontreal.CA (Jamorski Christine) Message-Id: <9401262030.AA00671@chims1.CHIMCN.UMontreal.CA> Subject: BIG Matrix Inversion To: chemistry@ccl.net (Computer Chemistry List) Date: Wed, 26 Jan 1994 15:30:42 -0500 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 157 Hello, We are looking for some code to do inversion of BIG Matrix... any references? Thank you! Christine Jamorski jamorskc@chims1.chimcn.umontreal.ca From saxena@physics.purdue.edu Wed Jan 26 16:44:50 1994 Received: from bohr.physics.purdue.edu for saxena@physics.purdue.edu by www.ccl.net (8.6.4/930601.1506) id PAA21486; Wed, 26 Jan 1994 15:52:46 -0500 Received: from localhost (saxena@localhost) by bohr.physics.purdue.edu (8.6.4/3.0) id PAA27709; Wed, 26 Jan 1994 15:53:40 -0500 Message-Id: <199401262053.PAA27709@bohr.physics.purdue.edu> Date: Wed, 26 Jan 1994 15:53:40 -0500 From: "Virendra K. Saxena" To: chemistry@ccl.net, jamorskc@CHIMCN.UMontreal.CA Subject: Re: BIG Matrix Inversion I have two small routines (one for real and other for complex) which I use for inverting matrices of upto 260X260 size. It workd pretty fast. If it can be useful to you, please send me an e-mail and I would be glad to send you the code. Goodluck V. K. Saxena saxena@physics.purdue.edu From alex@iqm.unicamp.br Wed Jan 26 16:46:00 1994 Received: from clio.iqm.unicamp.br for alex@iqm.unicamp.br by www.ccl.net (8.6.4/930601.1506) id QAA21804; Wed, 26 Jan 1994 16:22:33 -0500 Received: from localhost (alex@localhost) by clio.iqm.unicamp.br (8.6.4/8.3) id TAA00824; Wed, 26 Jan 1994 19:23:50 -0300 From: Alexandre Message-Id: <199401262223.TAA00824@clio.iqm.unicamp.br> Subject: Atomic Charges (GAMESS 93 vs. GAUSSIAN 92)! To: CHEMISTRY@ccl.net Date: Wed, 26 Jan 1994 19:23:49 -0300 (GMT-3:00) Cc: alex@iqm.unicamp.br X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 2354 Hello! I did a RHF/STO-3G geometry optimization in HCl, using GAUSSIAN 92. Then, I did a Mulliken population analysis, using GAUSSIAN 92. But, when I did the same calculation, using GAMESS 93, the Mulliken net charges were not the same! Why? I did the optimization geometry only with GAUSSIAN 92! *The GAUSSIAN 92 Input/Output is: ---------------------------------------------------- INPUT: ------ $rungauss #n rhf/sto-3g pop=reg ... HCl ... RHF/STO-3G 0 1 H Cl 1 r r 1.31333495 ---------------------------------------------------- OUTPUT: ------- ENERGY: HF=-455.1360117 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 1 .000000 .000000 -1.240372 2 17 .000000 .000000 .072963 ---------------------------------------------------------- Total atomic charges: 1 1 H .173622 2 Cl -.173622 Sum of Mulliken charges= .00000 ---------------------------------------------------- *The GAMESS 93 Input/Output is: ---------------------------------------------------- INPUT: ------ $CONTRL UNITS=ANGS $END $SYSTEM MEMORY=2000000 $END $BASIS GBASIS=STO NGAUSS=3 $END $DATA ... HCl ... RHF/STO-3G ... C1 H 1 .000000 .000000 -1.240372 Cl 17 .000000 .000000 .072963 $END ----------------------------------------------------- OUTPUT: ------- ENERGY: E(RHF) = -455.136011655 TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS ATOM MULL.POP. CHARGE LOW.POP. CHARGE 1 H .869767 .130233 .920083 .079917 2 CL 17.130233 -.130233 17.079917 -.079917 ----------------------------------------------------- Note that I used the same geometry in both calculations! And, in fact, the energy was practly the same! But the Mulliken charges... Does it represent a bug in GAMESS 93? Thanks! ------------------------------------ Alexandre Araujo de Souza. Universidade Estadual de Campinas Brazil. E-mail: alex@iqm.unicamp.br ------------------------------------ From YQIN@aardvark.ucs.uoknor.edu Wed Jan 26 16:46:38 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id QAA21559; Wed, 26 Jan 1994 16:00:42 -0500 From: Message-Id: <199401262100.QAA21559@www.ccl.net> Date: Wed, 26 Jan 94 15:01 CST Subject: How to get Hessian (in Gamess's format) from Gaussian-92? To: chemistry@ccl.net, chemistry-request@ccl.net, chemistry-search@ccl.net X-VMS-To: IN%"chemistry@ccl.net",IN%"chemistry-request@ccl.net",IN%"chemistry-search@ccl.net" Dear Netters: We are having problems getting the hessian in gamess format from gaussian92. We used the option Punch=Deriv,Gamess. According to the manual the keyword Deriv will give the energy and the first and second derivatives, however we are having trouble understanding the format that it gives. We were wondering if anyone a) understands this format and b)knows how to convert it into a form that gamess will read. This is a big problem. If you have any suggestions or hints please send them to me. Thank you very much. Qin From EDGECOMK@QUCDN.QUEENSU.CA Wed Jan 26 18:48:15 1994 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.4/930601.1506) id RAA22979; Wed, 26 Jan 1994 17:46:44 -0500 Message-Id: <199401262246.RAA22979@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 5940; Wed, 26 Jan 94 17:45:25 EST Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 0230; Wed, 26 Jan 1994 17:45:25 -0500 Date: Wed, 26 Jan 1994 17:40 EST From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: atomic charges Re: differences between G92 and GAMESS charges. The first thing to do here is to check to see that the integral accuracy is the same as well as the convergence criteria for the SCF. Other than that perhaps someone with more GAMESS experience (and G92 as well if there is a problem with the accuracy) can help. Take care. Ken Edgecombe From SBOESCH@aardvark.ucs.uoknor.edu Wed Jan 26 23:44:44 1994 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id XAA24764; Wed, 26 Jan 1994 23:01:58 -0500 From: Message-Id: <199401270401.XAA24764@www.ccl.net> Date: Wed, 26 Jan 94 22:02 CST Subject: How do you change g92 hessian into one that gamess will read? To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters: We are having trouble getting the hessian matrix into gamess format from gaussian 92. In the frequency calculation we are running in G92, we specify the keyword PUNCH=GAMESS,DERIV. According to the manual DERIV will give us the energy and first and second derivatives. The second derivative (the hessian) is what I am really interested in. The problem is we cannot understand the output in the fort.7 file. What we need to do is to take the hessian from this gaussian 92 calculation and transform it into gamess format and put it in a gamess input file to do another calculation. If anyone has any suggestions on how to do this, please tell us. Thank you. Scott Boesch sboesch@aardvark.ucs.uoknor.edu