From chemistry-request@server.ccl.net Tue Feb 15 03:09:17 2000 Received: from gatekeeper.mahindrabt.com ([202.54.20.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA18844 for ; Tue, 15 Feb 2000 03:09:03 -0500 Received: (from uucp@localhost) by gatekeeper.mahindrabt.com (8.9.3/8.8.6) with UUCP id LAA32275 for chemistry@ccl.net; Tue, 15 Feb 2000 11:58:29 +0530 Received: from mahindrabt.com ([10.5.2.69]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id LAA06770 for ; Tue, 15 Feb 2000 11:57:06 +0530 Message-ID: <38A8F1C8.D2BCD182@mahindrabt.com> Date: Tue, 15 Feb 2000 11:57:20 +0530 From: Sami Mukhopadhyay Organization: MBT,PUNE X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ASSIGNMENT OF ATOM TYPES IN MMFF94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL NETers, Assignment of atom types in MMFF94 ---------------------------------------- MMFF94 -- an atom based force field is known to be useful and is supported by many software packages in market. A naive study of the method -- especially for assigning atom types to C & N atoms-posed some problems for a beginner like me. Atoms in aromatic 5-rings are treated quite extensively in MMFF94. Types (38)NPYD and (39)NPYL are aromatic 5 ring N atoms with sigma and pi lone pair respectively. Type (65)N5A is for aromatic 5 ring N atom which is alpha to N: or O: or S: whereas (66)N5B is for aromatic 5 ring N atom which is beta to N: or O: or S: There is also an atom type (79)N5 which is general N in heteroaromatic 5-ring Similarly for carbon: Type (63)C5A is for aromatic 5 ring C atom which is alpha to N: or O: or S: whereas (64)C5B is for aromatic 5 ring C atom which is beta to N: or O: or S: There is also an atom type (78)C5 which is general C in heteroaromatic 5-ring The following questions arise from these facts: 1) If ring is a hetero-aromatic 5-ring, with respect to the base atom, only 4 atoms need to be addressed. Clearly 2 of them (the 2 atoms directly connected to base atom) will be alpha to the base atom, remaining 2 will be beta to the base atom. (If the hetero atom is N, it would be of type (39)NPYL. Hence, any other N in the same 5-ring will have the atom type (38)NPYD or (65)N5A or (66)N5B and C will have the atom type (63)C5A or (64)C5B. Any other type of carbon can't exist if 5-ring is an aromatic ring) In this situation, where do the types (78)C5 and (79)N5 fit? Can any one suggest me a structure in which atom types (78)C5 or (79)N5 would be used? 2) Coordination no. (i.e. no of attached atoms) for all the 3 types (38)NPYD, (39)NPYL and (79)N5 is [2]. How is this possible? e.g. in pyrrole, the nitrogen atom gets atom type (39)NPYL, then how does (39)NPYL have coordination no. [2]? Since, above mentioned problems were encountered by a non-chemist, there is a possibility of missed out facts. Can anybody put some light on this? Thanks in advance, -- Bhalchandra Gore From chemistry-request@server.ccl.net Tue Feb 15 06:52:18 2000 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA20644 for ; Tue, 15 Feb 2000 06:52:15 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id QAA00274; Tue, 15 Feb 2000 16:18:23 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id QAA11303; Tue, 15 Feb 2000 16:11:18 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Tue, 15 Feb 2000 16:11:18 +0530 (IST) From: Rajarshi Guha X-Sender: rajarshi@cts.iitkgp.ernet.in To: Mark Thompson cc: "'chemistry@ccl.net'" Subject: Re: CCL:Message software on Linux ? In-Reply-To: <86EDBD151558D311BB5700508B2E03FC01E47B03@pikachu.wrq.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, you could try MPI (Message Passing Interface) on Linux.As far as I know its used in parallel program implementations.This might be what you want =============================================================== Rajarshi Guha | ...but there was no one Dept. of Chemistry | in it........ IIT Kharagpur. | | RG. email: rajarshi@presidency.com | =============================================================== From chemistry-request@server.ccl.net Tue Feb 15 13:40:03 2000 Received: from mallard.duc.auburn.edu (mallard2.duc.auburn.edu [131.204.2.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA22132 for ; Tue, 15 Feb 2000 13:40:02 -0500 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id LAA03767 for ; Tue, 15 Feb 2000 11:35:04 -0600 (CST) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Tue, 15 Feb 2000 11:35:04 -0600 (CST) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: About solvation models Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers; I have little experienced about the solvation model caclulation. Would anyone give some suggestions on this matter? Also please recommend which method is effective and best. I will summarize it. Thank you in advance. Ohyun Kwon, graduate Department of Chemistry Auburn Universuty Auburn, AL 36849 USA From chemistry-request@server.ccl.net Tue Feb 15 16:16:00 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22808 for ; Tue, 15 Feb 2000 16:15:59 -0500 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id PAA04717 for ; Tue, 15 Feb 2000 15:10:59 -0500 (EST) Date: Tue, 15 Feb 2000 15:10:58 -0500 (EST) From: "Prof. John D Goddard" X-Sender: jgoddard@ccshst01 To: CHEMISTRY@ccl.net Subject: Pacifichem 2000 Symposium 125 Computational Quantum Chemistry (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Pacifichem 2000 Symposium 125 Computational Quantum Chemistry At the 2000 International Chemical Congress of Pacific Basin Societies in Honolulu, Hawaii, Dec. 14 - 19, 2000, Symposium 125 will be Computational Quantum Chemistry: Theoretical and Experimental Perspectives, in honour of Prof. Paul v. R. Schleyer on the occasion of his seventieth birthday. The coorganizers are: J. D. Goddard Guelph Canada Y. Osamura Rikkyo U. Japan L. Radom Australian National Australia H. F. Schaefer III Georgia USA P. Schwerdtfeger Auckland New Zealand M.W. Wong National University Singapore There will be seven half day sessions of invited oral presentations on computational organic chemistry, theoretical inorganic and organometallic chemistry, methods and applications of density functional theory, thermochemical predictions, and high level ab initio methods as well as other related topics. There will be a poster session to which your contributions are welcomed. You may submit your abstract for the Symposium 125 poster session at the American Chemical Society webpage http://www.acs.org/meetings/pacific2000 Scientists who have accepted invitations to speak in the symposium as of Feb. 15, 2000 include: R. Bartlett (Florida) A. Becke (Queens) R, Boyd (Dalhousie) W.T. Borden (Washington) E. Carter (UCLA) J. Chandrasekhar (Bangalore) J. Cioslowski (Florida State) T. Clark (Erlangen) M. Collins (Canberra) D. Dixon (PNL) J. Feng (Jilin) G. Frenking (Marburg) P.M.W. Gill (Cambridge) M. Gordon (Iowa State) J. Head (Hawaii) M. Head-Gordon (Berkeley) K. Hirao (Tokyo) K. Houk (UCLA) R. Kaiser (Acad.Sinica) N. Koga (Nagoya) Y.S. Lee (Korea AIST) Q. Li (Sichuan) R.G.A.R. Maclaglan (Canterbury,NZ) J.M.L. Martin (Weizmann Inst.)K. Morokuma (Emory) S. Nagase (Tokyo Metro.) E. Nakamura (Tokyo) T. Ohwada (Nagoya City) G. Olah (S.California) J.A. Pople (Northwestern) A. Rauk (Calgary) D, Salahub (NRC Ottawa) B. Salter-Duke (North.Terr..Australia) M. Saunders (Yale) H.B. Schlegel (Wayne State) P.v.R. Schleyer (Georgia) G. Scuseria (Rice) V.H. Smith, Jr. (Queens) Y. Wu (Hong Kong) D. Xie (Beijing Inst.Tech.) B. Yates (Tasmania) T. Ziegler (Calgary) From chemistry-request@server.ccl.net Tue Feb 15 16:17:51 2000 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22842 for ; Tue, 15 Feb 2000 16:17:51 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id MAA02459 for chemistry@ccl.net; Tue, 15 Feb 2000 12:23:15 -0800 From: Schrodinger Info account Message-Id: <200002152023.MAA02459@canter-n-siegel.schrodinger.com> Subject: CALL FOR PAPERS for MOPAC User Group (MUG) Meeting at ACS To: chemistry@ccl.net Date: Tue, 15 Feb 2000 12:23:15 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CALL FOR PAPERS for MOPAC User Group (MUG) Meeting at ACS Schrodinger, Compaq and Fujitsu are pleased to co-sponsor the first-ever Mopac Users Group (MUG) Meeting at 2pm - 5pm on March 25, 2000 at the Argent Hotel in conjunction with the Spring ACS Meeting in San Francisco. The MUG includes submitted presentations on chemistry and biochemistry applications of MOPAC (all versions) as well as a Q&A session with the author, Dr. J. J. P. Stewart. The full itinerary will be published shortly; currently, there are a few speaker's slots still available (20 minutes including questions). Please submit your complete contact information, title and an abstract of between 100 and 200 words to syl@schrodinger.com. For more information about submitting abstracts, and full details of the MUG, please visit www.schrodinger.com. From chemistry-request@server.ccl.net Tue Feb 15 23:20:27 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA25344 for ; Tue, 15 Feb 2000 23:20:27 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id TAA10471 for ; Tue, 15 Feb 2000 19:24:28 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Tue, 15 Feb 2000 19:24:28 -0800 (PST) From: Renxiao Wang To: CCL Subject: Gaussian free energy? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers! You know if you perform a frequency calculation with Gaussian, it will give you an "electronic and thermal free energy" in the log file. So my question is: what is this "free energy"? Or my question could also be described as: how does Guassian calculate the entropy? I hope some experts here know the answer. And please also explain to me to what problems I can apply this "free energy". Thanks a lot and I will put back the summary. ------------------------------------------------------------------------ | Dr. Renxiao Wang | ------------------------------------------------------------------------ | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | | University of California Los Angeles | Los Angeles, CA90066 | | Los Angeles, CA 90024 | U.S.A | | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | ------------------------------------------------------------------------ | E-mail: renxiao@chem.ucla.edu | | WWW: http://zimbu.chem.ucla.edu/~arthur/ | ------------------------------------------------------------------------