From lim@rani.chem.yale.edu Mon Feb 28 02:04:03 1994 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.4/930601.1506) id BAA25305; Mon, 28 Feb 1994 01:36:34 -0500 Received: by rani.chem.yale.edu; Mon, 28 Feb 94 01:36:18 -0500 From: Dongchul Lim Message-Id: <9402280636.AA10665@rani.chem.yale.edu> Subject: extracting normal modes from gaussian output To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 28 Feb 94 1:36:17 EST X-Mailer: ELM [version 2.3 PL11] Dear netters, There was a PERL utility which extracts vibratinal modes (for XMOL input) from gaussian frequency calculation output. This works perfect but I wrote it in AWK so that people who don't have PERL can use it. I guess this version will be more readable than PERL code. Do whatever you want with this. -DL I never used XMOL before. If the output doesn't work for XMOL, please let me know. ------------------- CUT HERE ------------------------------------------------- #!/usr/bin/nawk -f # @(#) g92vib: extracts vibrational modes from gaussian output for XMOL # Dongchul Lim, dlim@minerva.ycc.yale.edu # Usage: g92vib filename BEGIN { # initialize atomic symbols (add more rows if you need beyond Kr) nrows = 0; row[++nrows] = "H He"; row[++nrows] = "Li Be B C N O F Ne"; row[++nrows] = "Na Mg Al Si P S Cl Ar"; row[++nrows] = "K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr"; for(i=1;i<=nrows;i++) { n = split(row[i], s, " "); for(j=1;j<=n;j++) symbol[nsymbol+j] = s[j]; nsymbol += n; } natoms = 0; } # get either Z-Matrix orientation or Standard orientation. # if both are present, Standard orientation will be used, since # it is found later than Z-Matrix orientation in Gaussian output. /(Z-Matrix orientation:|Standard orientation:)/ { natoms = 0; for(i=1;i<=4;i++) getline; # skip 4 lines while (1) { getline; if (match($0, "---")) break; if ($2 <= 0) continue; # skip dummies natoms++; an[natoms] = $2; x[natoms] = $3; y[natoms] = $4; z[natoms] = $5; } next; } # look for Harmonic frequencies /Harmonic frequencies/ { if (natoms == 0 ) { printf("Standard orientation / Z-Matrix orientation not found.\n"); exit; } # skip two lines getline; getline; nfreq = 0; while (1) { getline; if (match($0, "Harmonic") != 0) break; getline; # read in frequencies getline; nf = split(substr($0, 24), freq, " "); # skip 6 lines for(i=1;i<=6;i++) getline; # read in normal mode vectors for(i=1;i<=natoms;i++) { getline; for(j=1;j<=nf;j++) xmode[i,j] = $(j+3); getline; for(j=1;j<=nf;j++) ymode[i,j] = $(j+3); getline; for(j=1;j<=nf;j++) zmode[i,j] = $(j+3); } # print out coords and normval mode vectors for each mode for(i=1;i<=nf;i++) { nfreq++; file = sprintf("%s.nu%02d", FILENAME, nfreq); printf("%d\n", natoms) > file printf("NU=%.3f\n", freq[i]) > file for(j=1;j<=natoms;j++) { sym = (an[j] <= 0 || an[j] > nsymbol) ? "X" : symbol[an[j]]; printf(" %2s % 12.6f % 12.6f % 12.6f % 12.6f % 12.6f % 12.6f\n", sym, x[j], y[j], z[j], xmode[j,i], ymode[j,i], zmode[j,i]) > file } close(file); } } exit; } ------------------- CUT HERE ------------------------------------------------- From ferenc@rchsg8.chemie.uni-regensburg.de Mon Feb 28 03:04:06 1994 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id CAA25539; Mon, 28 Feb 1994 02:33:48 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA12875; Mon, 28 Feb 94 08:33:42 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA25474; Mon, 28 Feb 94 08:35:27 +0100 Date: Mon, 28 Feb 94 08:35:27 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9402280735.AA25474@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: borland Dear Netters, a friend of mine is looking for a BORLAND newsgroup or something similar. He is interested in obtaining BGI-drivers for the S3 and TIGA video boards. He is quite frustrated about BORLANDs hotline: "Please wait, the next free line is yours ...", continuing for hours. Does anybody know about such a newsgroup? Thank you very much in advance. Best regards, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From jabs@chemie.uni-halle.d400.de Mon Feb 28 05:04:24 1994 Received: from ixgate02.dfnrelay.d400.de for jabs@chemie.uni-halle.d400.de by www.ccl.net (8.6.4/930601.1506) id EAA26502; Mon, 28 Feb 1994 04:27:37 -0500 From: X400-Received: by mta d400relay in /PRMD=dfnrelay/ADMD=d400/C=de/; Relayed; Mon, 28 Feb 1994 10:27:55 +0100 X400-Received: by /PRMD=UNI-HALLE/ADMD=D400/C=DE/; Relayed; Mon, 28 Feb 1994 10:26:04 +0100 Date: Mon, 28 Feb 1994 10:26:04 +0100 X400-Originator: jabs@chemie.uni-halle.d400.de X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=UNI-HALLE/ADMD=D400/C=DE/;mlumta1076940228102604-CCG] X400-Content-Type: P2-1984 (2) Message-ID: <940228102603*/S=jabs/OU=chemie/PRMD=UNI-HALLE/ADMD=D400/C=DE/@MHS> To: CHEMISTRY@ccl.net Subject: positions offered Dear Netters, i am looking for lists 'positions offered' in the field of NMR spectroscopy and general biochemistry. Please e-mail to jabs@cis.biochemtech.uni-halle.de Thanks in advance, Andreas ------------------------------------------------------------------- Andreas Jabs MP-AGr. Enzymologie der Peptidbindung Weinbergweg 16a 06120 Halle/Saale GERMANY phone +49 345 617246 fax +49 345 647126 e-mail jabs@cis.biochemtech.uni-halle.de ------------------------------------------------------------------- jabs@cis:110> From Keith.Refson@earth.ox.ac.uk Mon Feb 28 06:04:08 1994 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id FAA26852; Mon, 28 Feb 1994 05:30:45 -0500 From: Keith Refson Received: from rahman.earth.ox.ac.uk by earth.ox.ac.uk; Mon, 28 Feb 94 10:31:23 GMT Date: Mon, 28 Feb 94 10:31:19 GMT Message-Id: <26135.9402281031@rahman.earth.ox.ac.uk> To: CHEMISTRY@ccl.net Subject: MD program, "Moldy" Last week somebody posted a message to this list about my MD code, moldy. I discovered this when, to my surprise I saw that it had been downloaded 46 times in three days! I am gratified to see such interest, and very happy to make it generally available to the scientific community. There are a few points I would like to make, the most important one first. I am keeping an "announcements only" list of email addresses of anyone who uses the program for notification of updates, bugs, fixes and so forth. Please contact me if you would like to be added to this list, by email to Keith.Refson@earth.ox.ac.uk. Second, here's a bit more about what the program does, extracted from the README files in the distribution: Moldy is a general-purpose molecular dynamics simulation program which I wrote initially for my own research into aqueous solutions at mineral surfaces. However it is sufficiently flexible that it ought to be useful for a wide range of simulation calculations of atomic, ionic and molecular systems. It is targetted at solids and liquids, and does not (in the current version) allow for molecular flexibility which restricts is appicability for biomolecular purposes. The source code is available by anonymous file transfer from Oxford. Connect to "earth.ox.ac.uk" using "ftp", with an account name of "anonymous" and your email address as password. The relevant files are all in the "/pub" directory and are * moldy-2.6.tar.Z - The Unix distribution (also for MSDOS) * moldy-2.6.com - The VMS distribution * moldy-manual.ps.Z - The Manual in PostScript form. Note that the distribution files already contain the LaTeX source. The PostScript version of the manual is for those who don't have LaTeX installed on their systems. The distribution files already contain the LaTeX source. Third, I welcome any comments, suggestions, example system specification files you have, and in particular any improvements you make to the program. Finally, if you publish a paper in a scientific journal where any of the work described used "moldy" I would must ask you to include a small ackowledgement for the use of the program. Keith Refson ------------------------------------------------------------------------------ | Email : keith@earth.ox.ac.uk | Dr Keith Refson | | UUCP : ...!mcsun!uknet!ed!K.Refson| Department of Earth Sciences | | PHONE(FAX): +44 865 272026 (272072) | Parks Road, Oxford OX1 3PR, UK | ------------------------------------------------------------------------------ From nittoli@pokey.chem.sunysb.edu Mon Feb 28 11:05:27 1994 Received: from pokey.chem.sunysb.edu for nittoli@pokey.chem.sunysb.edu by www.ccl.net (8.6.4/930601.1506) id KAA29703; Mon, 28 Feb 1994 10:58:58 -0500 Received: by pokey.chem.sunysb.edu (911016.SGI/920502.SGI) for chemistry@ccl.net id AA24957; Mon, 28 Feb 94 16:05:56 GMT Date: Mon, 28 Feb 94 16:05:56 GMT From: nittoli@pokey.chem.sunysb.edu (Thomas Nittoli) Message-Id: <9402281605.AA24957@pokey.chem.sunysb.edu> To: chemistry@ccl.net Subject: SESAM Protein Information System Hello Everyone, Recently I have asked for information about a program called SESAM or SYBASE (Proteins: Structure, Function, and Genetics 11:59-76 (1991)). I have summarized the replies below (if anyone would like the actual replies just send me an e-mail message): 1. In a recent paper by G. Vriend, C. Sander & P.F.W. Stouten ("A Novel Search Method for Protein Sequence- Structure Relations, Using Property Profiles," Protein Eng. 7 (1994) 23) they show that relational databases are unsuitable and provide an alternative. 2. SYBASE is a ~$5000 commercial relational database package (address of SYBASE included) that SESAM is implemented on. It could also be implemented under ORACLE. 3. Potential contact(s) for Prof. Wodak 4. Potential license agreement and a nominal fee for SESAM. Thank you to everyone who replied (P.Stouten, B.Davies, J.Nauss, and C.S.Raman) and the CompChem exploder. ___________________________________________ Thomas Nittoli Dept. of Chemistry State University of NY Stony Brook, NY 11794-3400 USA Phone: (516)632-7854 FAX: (516)632-7960 Internet: nittoli@pokey.chem.sunysb.edu From kkemete1@gwdg.de Mon Feb 28 14:04:15 1994 Received: from gwdu17.gwdg.de for kkemete1@gwdg.de by www.ccl.net (8.6.4/930601.1506) id NAA01250; Mon, 28 Feb 1994 13:09:03 -0500 Received: from gwdu12.gwdg.de by gwdu17.gwdg.de with SMTP (PP); Mon, 28 Feb 1994 19:12:13 +0100 Received: by gwdu12.gwdg.de (5.57/ultrix-gwdg) id AA10086; Mon, 28 Feb 94 19:07:59 +0100 From: kkemete1 Message-Id: <9402281807.AA10086@gwdu12.gwdg.de> Subject: CharM/Quanta on HP with CRX24Z To: CHEMISTRY@ccl.net Date: Mon, 28 Feb 1994 19:07:58 +0100 (MET) Content-Type: text Content-Length: 705 Dear Netters! We would like to animate the trajectories of our simulations and plan to do this with Quanta from MSI. Has anyone experiences with the programs CharmM/Quanta running on HP-workstations - let's say a 715/75 with the CRX-24Z-Adapter? Any information is very welcomed. Thanks Karsten -- Karsten Kemeter ::::::::::::::::::::::::::::::::::::::::::::::::::::::: | Max-Planck-Institut fuer Biophysikalische Chemie | | Abteilung Laserphysik | | | | Am Fassberg | | 37077 Goettingen | | | | Tel.: xx49/551/201-339 | | FAX.: xx49/551/201-341 | | e-mail: kkemete1@gwdg.de | ::::::::::::::::::::::::::::::::::::::::::::::::::::::: From Don_Gregory@MSI.COM Mon Feb 28 16:04:16 1994 Received: from schizoid.msi.com for Don_Gregory@MSI.COM by www.ccl.net (8.6.4/930601.1506) id PAA03345; Mon, 28 Feb 1994 15:48:08 -0500 Received: from msi.com (qmail-gw.msi.com) by schizoid.msi.com (4.1/SMI-4.1) id AA05517; Mon, 28 Feb 94 15:47:36 EST Message-Id: <9402282047.AA05517@schizoid.msi.com> Date: 28 Feb 1994 15:45:20 +0000 From: "Don Gregory" Subject: re- MD anim. on Quanta/HP To: "CHEMISTRY BBS" Subject: Time:3:14 PM OFFICE MEMO re: MD anim. on Quanta/HP Date:2/28/94 Karsten Kemeter of the Max-Plank-Institute asked about running molecular dynamics animations on the HP using Quanta/CHARMm. At MSI we have had very good results doing just that. The only qualification, in general (Karsten is already in good shape, but for the rest of those who may be interested) is to ensure the minimum configuration. This I give below: For the HP 9000 (700 series) HP-UX 9.0.1 operating system 32MB memory and 24CRXZ or 48CRXZ graphics option With that, you'd be in good shape. I hope anyone out there who has an HP configured minally above is achieving satisfactory results; we have generally heard excellent reviews by our curstomers using HP systems. If anyone has any technical questions on the above, you could contact the MSI support hotline: 1-800-756-4674 or support@msi.com Don Gregory Mgr. Application Science MSI From YQIN@aardvark.ucs.uoknor.edu Mon Feb 28 17:04:16 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id QAA03847; Mon, 28 Feb 1994 16:37:26 -0500 From: Message-Id: <199402282137.QAA03847@www.ccl.net> Date: Mon, 28 Feb 94 15:36 CST Subject: g92 in SGI To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters: I have some difficulty to compile g92 in our SiliconGraphic (IRIS Indigo) workstation. I checked the disc space and smake file, it doesn't seem to have any problem. I attracted both bldg92.log and anything showed on the screen when I compiled g92. Because thoese two files too larger to post. I would appreciate it very much if someone can help me out. Any commem or suggestions would be a great help. Thank you very much in advarce yueyi qin From jle@world.std.com Mon Feb 28 19:04:17 1994 Received: from relay1.UU.NET for jle@world.std.com by www.ccl.net (8.6.4/930601.1506) id SAA05091; Mon, 28 Feb 1994 18:41:23 -0500 Received: from world.std.com by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwfgo09481; Mon, 28 Feb 94 18:41:07 -0500 Received: by world.std.com (5.65c/Spike-2.0) id AA12458; Mon, 28 Feb 1994 18:41:05 -0500 Date: Mon, 28 Feb 1994 18:41:05 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199402282341.AA12458@world.std.com> To: chemistry@ccl.net Subject: Slater Zeta's for elements n > 36? Does anybody have zeta's for elements beyond Krypton on the periodic table? I've got them through Kr, but need them through Xe (at least). References are good, but on-line info's better... I have the orbital breakdown through Kr in an OLD copy of Karplys and Porter - are there more in a newer one? Shows my age... Joe Leonard jle@world.std.com