From dam@retina.chem.psu.edu Wed Dec 22 10:19:38 1993 Received: from retina.chem.psu.edu for dam@retina.chem.psu.edu by www.ccl.net (8.6.4/930601.1506) id JAA16817; Wed, 22 Dec 1993 09:47:22 -0500 Received: by retina.chem.psu.edu (920110.SGI/1.30) (for chemistry@ccl.net) id AA19267; Wed, 22 Dec 93 09:46:46 -0500 Date: Wed, 22 Dec 93 09:46:46 -0500 From: dam@retina.chem.psu.edu (K.V. Damodaran) Message-Id: <9312221446.AA19267@retina.chem.psu.edu> To: chemistry@ccl.net Subject: United Atom ESP-fit charges from Gaussian-92 Dear Netters, Does anyone know the keyword for calculating the united atom ESP-fit charges using Gaussian-92 ? I tried Pop=MK, but this gives only the "all atom" charges. Please email to dam@retina.chem.psu.edu Thanks for your help K.V. Damodaran From stoutepf@chemsci1.es.dupont.com Wed Dec 22 11:19:41 1993 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.4/930601.1506) id KAA17262; Wed, 22 Dec 1993 10:26:08 -0500 Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991); id AA19119; Wed, 22 Dec 93 10:26:07 -0500 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com (4.1/SMI-4.1) id AA14495; Wed, 22 Dec 93 10:24:31 EST Message-Id: <9312221524.AA14495@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Wed, 22 Dec 1993 10:25:12 -0500 To: DIBUG@comp.bioz.unibas.ch, chemistry@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: L-J parameters for Calcium ion On Tue, 21 Dec 1993, Bill Ross wrote: >A word of warning for those converting the A,B form parameters to r*,eps: > >The simple translation formulas one can derive to map A,B to r*,epsilon >set the potential to be the same between atoms of the given type under >both conventions. BUT, note that owing to the different combining rules >associated with these two forms of notation, the per-atom potentials derived >this way result in different distances of the minimum for pairs of atoms >of _different_ types [...] > I should have provided all data. Bartolotti et al. give for calcium r* = 1.74 A, eps = 0.0465 kcal/mol, C6 = 2.58 kcal A^6/mol, C12 = 35.8 kcal A^12/mol. Apart from the fact that they reproduce hydration free energy differences well, the attraction of Bartolotti's C6 parameters (pun not intended) is that they are not optimized in any sense but derived straight from the hydrodynamic formulation of time-dependent Kohn-Sham theory (don't ask me what that means). Happy Holidays, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- ARA/Fax: +1 (302) 695 4324 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From dqujfm0@PS.UIB.ES Wed Dec 22 12:19:43 1993 Received: from sc.uib.es for dqujfm0@PS.UIB.ES by www.ccl.net (8.6.4/930601.1506) id MAA18895; Wed, 22 Dec 1993 12:01:56 -0500 Received: from EAN_GATE by SC.UIB.ES (PMDF #12442) id <01H6SDTNMTB400106X@SC.UIB.ES>; Wed, 22 Dec 1993 17:21 1 Date: Wed, 22 Dec 1993 17:21:53 UTC+0200 From: Juan Frau Subject: Information ECCC1 To: chemistry@ccl.net Message-id: <86*dqujfm0@PS.UIB.ES> Content-identifier: 86 Conversion: Prohibited X400-content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=es/ADMD=/C=/;931222172153] X400-received: by /PRMD=es/ADMD=/C=/; Relayed; Wed, 22 Dec 1993 17:21:53 UTC+0200 X400-recipients: non-disclosure:; X400-Originator: dqujfm0@PS.UIB.ES Net, I am interested in participate in First European Conference on Computational Chemistry (Nancy. 23-27 May). However I can not to connect with the fax number (33) 43 31 59 45. Can you tell me if this number is wrong? Thanks in advance. Juan Frau Universitat Illes Balears. Palma. Spain Fax : 34 71 17 34 26 Email: dqujfm0@ps.uib.es From walt@ibm1.carb.nist.gov Wed Dec 22 14:20:55 1993 Received: from ENH.NIST.GOV for walt@ibm1.carb.nist.gov by www.ccl.net (8.6.4/930601.1506) id NAA21708; Wed, 22 Dec 1993 13:48:34 -0500 Received: from ibm1.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01H6S6FBMW2O003VTF@ENH.NIST.GOV>; Wed, 22 Dec 1993 13:48:42 EDT Received: by ibm1.carb.nist.gov (AIX 3.2/UCB 5.64/4.03) id AA14608; Wed, 22 Dec 1993 13:50:18 -0500 Date: Wed, 22 Dec 1993 13:48:43 -0500 (EST) From: "Dr. Walter J. Stevens" Subject: Background Computing To: Chemistry List Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Netters, Does anyone know if it is possible to set up a true "sponge" queue for background computing on IBM RS/6000 and SGI workstations? We have found that a 'nice' priority of 19 (relative to 0) doesn't provide enough discrimination between high priority and background jobs. We have a lot of unused machine cycles if we could get at them without interfering with interactive and priority work. Thanks. -------------------------------------------------- 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 mercie@med.cornell.edu Wed Dec 22 14:23:06 1993 Received: from cumc.cornell.edu for mercie@med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id NAA21704; Wed, 22 Dec 1993 13:48:24 -0500 Received: from localhost (mercie@localhost) by cumc.cornell.edu (8.6.4/ECH1.13) id NAA25879; Wed, 22 Dec 1993 13:46:41 -0500 Date: Wed, 22 Dec 1993 13:46:41 -0500 (EST) From: Gustavo Mercier Subject: Re: L-J parameters for Calcium ion To: JWANG@ac.dal.ca cc: chemistry@ccl.net In-Reply-To: <01H6QY991RXE003TZS@AC.DAL.CA> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 21 Dec 1993 JWANG@ac.dal.ca wrote: > > I am trying to do some MD simulations involved Calcium ions, but I cannot > find the parameters (sigma and epsiron) of the LJ potential for the ion. > Could anyone provide me these parameters or give me a hint so that I can > find these data. Also any comment about the simulation of Ca2+ is very > I don't have the reference with me but Dr. Harel Weinstein and Dr. Kenzi Hori generated parameters for Calcium to be used with Charmm. Look for references in the mid to late 80's or early 90's. Dr. Alan Factor used these parameters in his doctoral dissertation on Calmodoulin. Dr. Weinstein is the chairman of Physiology and Biophysics, Mount Sinai School of Medicine, NY, NY. Unfortunately, I don't have his e-mail address. Dr. Hori is back in Japan after doing post - doc work with Dr. Weinstein. Let me know if you can get in touch with them. I may be able to help. gus mercier mercie@cumc.cornell.edu From jkl@ccl.net Wed Dec 22 16:19:43 1993 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id PAA22542; Wed, 22 Dec 1993 15:31:58 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id PAA02500; Wed, 22 Dec 1993 15:31:58 -0500 Date: Wed, 22 Dec 1993 15:31:58 -0500 Message-Id: <199312222031.PAA02500@krakow.ccl.net> To: chemistry@ccl.net Subject: Greetings to all Cc: jkl@ccl.net Dear Netters, I look around and see people sneaking out of work to do some last minute shopping. What tells me that it is time... I wish you all the best during this Holiday Season. Though my wishes may come a little too late or a little too early for some, they are all the same and sincere. Have the best in the New Year too. I wish you plenty of new achievement in your personal careers, I wish you all to be blessed with good health and happiness. And when we hear the last chime of the bell let us not say "another year passed..."; let us say "a new and exciting year is coming...". + XXX XXXXX XXXXXXX XXXXXXXXX "BOAS FESTAS" "JOYEUX NOEL" "VESELE VANOCE" "MELE KALIKIMAKA" "NODLAG SONA DHUIT" "BLWYDDYN NEWYDD DDA" "GOD JUL" "BUON ANNO" "FELIZ NATAL" "FELIZ NAVIDAD" "MERRY CHRISTMAS" "KALA CHRISTOUGENA" "VROLIJK KERSTFEEST" "FROHLICHE WEIHNACHTEN" "BUON NATALE-GODT NYTAR" "HUAN YING SHENG TAN CHIEH" "WESOLYCH SWIAT-SRETAN BOZIC" "MOADIM LESIMHA-LINKSMU KALEDU" "HAUSKAA JOULUA-AID SAID MOUBARK" "'N PRETTIG KERSTMIS" "ONNZLLISTA UUTTA VUOTTA" "Z ROZHDESTYOM KHRYSTOVYM" "NADOLIG LLAWEN-GOTT NYTTSAR" "FELIC NADAL-GOJAN KRISTNASKON" "S NOVYM GODOM-FELIZ ANO NUEVO" "GLEDILEG JOL-NOELINIZ KUTLU OLSUM" "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC" "KRIHSTLINDJA GEZUAR-KALA CHRISTOUGENA" "SELAMAT HARI NATAL - LAHNINGU NAJU METU" "SARBATORI FERICITE-BUON ANNO" "ZORIONEKO GABON-HRISTOS SE RODI" "BOLDOG KARACSONNY-VESELE VIANOCE " "MERRY CHRISTMAS - - HAPPY NEW YEAR" "ROOMSAID JOULU PUHI -KUNG HO SHENG TEN" "FELICES PASUAS-EIN GLUCKICHES NEWJAHR" "PRIECIGUS ZIEMAN SVETKUS SARBATORI VESLLE" "BONNE ANNEBLWYDDYN NEWYDD DDADRFELIZ NATAL" XXXXX XXXXX XXXXX XXXXXXXXXXXXX Jan Labanowski CCL coordinator jkl@ccl.net From rec@ncifcrf.gov Wed Dec 22 17:19:41 1993 Received: from fcs280s.ncifcrf.gov for rec@ncifcrf.gov by www.ccl.net (8.6.4/930601.1506) id QAA23192; Wed, 22 Dec 1993 16:31:35 -0500 From: Received: from fcindy5.ncifcrf.gov by fcs280s.ncifcrf.gov (4.1/NCIFCRF-3.0/AWF-2.0) id AA08673; Wed, 22 Dec 93 16:23:34 EST Received: by fcindy5.ncifcrf.gov (920330.SGI/911001.SGI) for @fcs280s.NCIFCRF.GOV:chemistry@ccl.net id AA04469; Wed, 22 Dec 93 16:13:56 -0500 Date: Wed, 22 Dec 93 16:13:56 -0500 Message-Id: <9312222113.AA04469@fcindy5.ncifcrf.gov> To: chemistry@ccl.net Subject: News on MOPAC-DOS Reply-To: cachau@ncifcrf.gov Hi!, Some people complain they got a corrupted version of the MOPAC for DOS. Ivar just download a new copy on my machine, which seems to have the right byte count, (and I just tested and seems to work fine). The only difference with the original copy is that this one is a bit more wordy. I run the standard water test and works smoothly. REMEMBER to download the files in _binary_ mode!. There is a new address you can use. The first one suppose to be faster. If you experience any problems with this address try the second one, the files are still in there. The Mopac for DOS can be found at: fconvx.ncifcrf.gov (129.43.52.4); subdirectory: ./tmp/mopac_dos or fcindy5.ncifcrf.gov (129.43.9.58); subdirectory: ./mopac_dos Login "anonymous" and enter your e-mail address as password. Good Luck REC _____________________________________________________________________________ Raul E. Cachau, National Cancer Institute Frederick Cancer Research and Development Center, PRI/DynCorp Structural Biochemistry Program and Frederick Biomedical Supercomputer Center Building 322, Room 19, P.O.Box B, Frederick, MD 21702-1201, USA Phone: +1-(301)-846-6062; Fax: +1-(301)-846-6066; e-Mail: cachau@ncifcrf.gov _____________________________________________________________________________ From budong@chem.columbia.edu Wed Dec 22 18:19:50 1993 Received: from cucbs.chem.columbia.edu for budong@chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id SAA24109; Wed, 22 Dec 1993 18:17:06 -0500 Received: by cucbs.chem.columbia.edu id AA15648 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 22 Dec 1993 18:16:51 -0500 Date: Wed, 22 Dec 1993 18:16:51 -0500 From: Budong Peng Message-Id: <199312222316.AA15648@cucbs.chem.columbia.edu> To: chemistry@ccl.net Subject: GAMESS plotting: DENDIF for two sets and specific orbitals Dear Netters; I was trying to plot our the electronic density difference of two molecules, and especially for one or several orbitals. I followed the instruction from dendif.man, e.g., 'dendif' a formamide-H2O complex, and 'dendif' the formamide only (with geometry identical to that in the complex), and put MINUS=1 in the first .ddf file, with TWO TWO for PSISQR and SUBDEN, but it didn't work. The manual is as the following: ****************************************************************** @PSISQR {TWO|ONE|:} ---------------------------------------------------------- This card gives the electron occupation numbers of all the orbitals occupied in the whole molecule. The actual number of orbitals is read from the whole molecule's PLTORB file. If all occupation numbers are 2.0 or 1.0, a single shorthand keyword may be used. ---------------------------------------------------------- @SUBDEN: [TWO|ONE|:] ---------------------------------------------------------- *** Repeat this read site MINUS times. This is the occupation number of each natural orbital occupied in a fragment of the whole molecule. The meanings are the same as @PSISQR. ******************************************************************** I tried various formats for these two groups when I don't have identical occupation, but failed to figure out the right one. ******************************************************************** The remaining input is read from the various PLTORB disk files. You must run PLTORB a total of MINUS+1 times. The whole molecule's data is provided on unit 20, and the various fragments are read in from units 21, 22, 23, ..., with their electron occupancies provided @SUBDEN in the exact same order. ******************************************************************* I followed this part, if it doesn't mean that I have support all the parts. What's more, if I wnat to plot several orbitals, say, mostly related with the original O 2p orbitals, can I do that? Any suggestions and advice are greatly appreciated. Merry Christmas to you all. Budong Peng From berkley@wubs.wustl.edu Wed Dec 22 19:19:42 1993 Received: from wugate.wustl.edu for berkley@wubs.wustl.edu by www.ccl.net (8.6.4/930601.1506) id SAA24346; Wed, 22 Dec 1993 18:21:50 -0500 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA06260; Wed, 22 Dec 1993 17:21:33 -0600 Received: by wubs.wustl.edu; (5.65/1.1.8.2/14Oct93-1217PM) id AA15631; Wed, 22 Dec 1993 17:24:28 -0600 Date: Wed, 22 Dec 1993 17:24:28 -0600 From: "Mr. Berkley Shands" Message-Id: <9312222324.AA15631@wubs.wustl.edu> To: chemistry@ccl.net Subject: Energy Code in C I'm looking for any code to calculate energies, written in C, given the X-Y-Z coordinates of a set of atoms, and their atom types. It does NOT have to be fancy, only produce an "energy" number for comparing conformations. Thanks in advance, Berkley Shands