From K360171@ALIJKU11.bitnet Fri Feb 12 04:26:05 1993 Message-Id: <199302120854.AA25610@oscsunb.ccl.net> Date: Fri, 12 Feb 93 09:48:41 CET From: Norbert Mueller Subject: mac PDB graphics To: chemistry@ccl.net Following up on recent requests in this list I would like to convey the following information: I have been developing such a program for the last years, it is called Ball & Stick and is now available commercially from Cherwell Scientific Publishing 15 Auburn Place Brookline MA 02146 Tel: (617) 277 4200 Fax: (617) 739 4836 They also have a free demo, which is also available by ftp from sumex-aim.stanf in the info-mac/demo directory. Note the demo is limited to 40 atoms, I have use full version for pdb files with more than 10000 atoms. Norbert Mueller Institute of Chemistry Johannes Kepler University A-4040 Linz AUSTRIA From topper@haydn.chm.uri.edu Fri Feb 12 04:36:41 1993 Date: Fri, 12 Feb 93 09:36:41 -0500 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9302121436.AA09629@haydn.chm.uri.edu> To: chemistry@ccl.net Subject: Re: scaled frequencies for S and H >Leif Haldor writes: >You have to scale the frequencies you get from Gaussian by about 0.9. >The enthalphy, entropy and ZPE among other thermodynamical properties >calculated by Gaussian depend upon the frequencies. Does someone on this >list know how you can compute the thermodynamical properties using scaled >frequencies in Gaussian? Probably not possible? If so, has someone written >a program to extract the frequencies from the outputfile or chk-file, >correct for the scaling and then compute the thermodynamical properties? >Or do I have to use Lotus 1-2-3 or Excel after looking up the litterature >references for all the formulas. >Robert Topper responds: >You can certainly estimate thermochemical properties from the frequencies >you get from Gaussian. However, you will have to use the rigid-rotator/ >harmonic oscillator (RRHO) approximation to the partition function, which >requires the three principal moments of inertia as well as the >harmonic frequencies. These can be calculated from the molecular >geometry and masses. Also, the calculation may only >be semi-quantitative, unless you have a fancy way of estimating the >partition function. (Significantly more and detailed information has been deleted from this response - DAS.) And Doug Smith adds: >In a recent manuscript we wrote: >"Each HF/6-31G* optimization, and for the monomers the MP2/6-31G* >optimizations, were followed by normal frequency analysis to make sure an >energy minimum was obtained and for calculating free energies at 298 >K and one atmosphere. In the free energy calculations the thermal >correction to the enthalpy, H(T) and entropy, S(T) were calculated in the >rigid rotor, harmonic oscillator approximation. Ideal gas behavior >was accepted in the imidazole protonation reaction and for the formation >of monohydrates. The thermal energy contributions were calculated using >classical statistical thermodynamic functions. The total entropy >for PyW(pi) and Im(3)W without any molecular symmetry contain a term >of RTln2 due to the entropy of mixing." >Taken from: Nagy, P. I.; Durant, G. J.; Smith, D. A. "Theoretical Studies >on Hydration of Pyrrole, Imidazole and Protonated Imidazole in the Gas >Phase and Aqueous Solution," J. Am. Chem. Soc., in press. >Doug Doug, Please understand that I have nothing agains the classical rigid-rotator/quantum harmonic-oscillator approximation, which enjoys widespread use. (A paper I saw by J. Gao on the Menshutskin reaction [JACS 113, 7796 (1991)] comes to mind). Also, Don Truhlar (with whom I did the quantum Monte Carlo work) and Bruce Garrett have been using this approximation for many years in rate constant and isotope effect calculations for polyatomic molecules, often with great success. However, if a molecule can undergo internal rotations at room temperature, or the molecule is an ionic complex of some kind (large-amplitude, low-frequency stretches), the CRR/QHO approximation has less chance of working well. Moreover, anharmonicities can sometimes have a big effect on the zero-point energy, and thus affect the quality of the thermochemical calculations. This is my main point...and the point of our JCP article. My second point is that the use of scaled freqencies may be numerically justified, but has never been actually tested against exact calculations of free energies, at least not to my knowledge. Personally, if I were going to calculate thermochemical properties from a Gaussian calculation, I'd use the classical rigid rotator for the rotations, calculate some cubic and quartic force constants using Gaussian (assuming I had enough computer time), and use the expression given for the vibrational partition function in Truhlar and Issacson, JCP 94, 357 (1991). At least then the zero-point energy would be accurate, and so then presumably would be the room-temperature thermochemical values (again, assuming no internal rotations....). Moreover, only a subset of the force field is needed for the aforementioned approximate form. -rqt ******************************** * Robert Q. Topper, Ph.D. * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * rtopper@chm.uri.edu OR * * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** From compchem@quinor.edu.ar Fri Feb 12 10:28:47 1993 Date: Fri, 12 Feb 1993 13:28:47 -0300 From: Message-Id: <445bl569@quinor.edu.ar> To: chemistry@ccl.net Subject: 7th Latinamerican School on Theoretical Chemistry 7th Latinamerican School on Theoretical Chemistry La Plata, Province of Buenos Aires, Argentine 20-26th February 1994 The 7th edition of the Latinamerican School on Theoretical Chemistry is being organized by Programa Quinor, Quimica Inorganica, Faculty of Exact Sciences, University of La Plata and will be held at this university on 20-26th February 1994. The 7th LSTCh will have four courses with intensive theory and practice: 1) Electronic Molecular Structure: Calculation Methods. 2) Density Functional Theory and Chemical Reactivity. 3) Pharmacology. 4) Molecular Spectroscopy. Courses 1 and 2 will be given simultaneously. The same is valid for courses 3 and 4. Thus, the attendees will have to choice only two courses to take. The 7th LSTCh is intended for graduate and advanced under-graduate students on Chemistry, Physics, Mathematics and Engineering. Depending on availability of funds, fellowships may be available to help participant expenses (registration fee not included). The language of the school will be Spanish. Registration fee: U$S 50. Further information and pre-registration form to: Prof. Eduardo A. Castro 7th LSTCh Programa Quinor, Quimica Inorganica, FCE, UNLP CC 962, CP 1900, La Plata, Argentina Phone: 54-21-21 40 37 54-21-25 94 85 Fax: 54-21-25 94 85 E-mail: castro@quinor.edu.ar ====================================================================== Pre-registration form 7th LSTCh, La Plata, Argentina, 20-26th February 1994 Complete Name: Institution: Address: Phone: Fax: E-mail: Fellowship required (if any)?: yes no Lodging reservation required?: yes no Which courses would you take during the school? (indicate numbers) CompChem@quinor.edu.ar From rs0thp@RohmHaas.Com Sat Feb 13 49:08:43 1993 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9302121945.AA20035@monte.br.RohmHaas.Com> Subject: W. Clark Still Award Banquet-Mar.30 7:30pm To: chemistry@ccl.net Date: Fri, 12 Feb 1993 14:45:43 +22305823 (EST) Dear Folks, I hope at least some of you are going to the Denver ACS meeting. At this meeting Prof. W. Clark Still will recieve the ACS Award for Computers and Chemistry sponsored by Digital Equipment, and Prof. Martin Karplus will receive the ACS Award for Theoretical Chemistry sponsored by IBM. Both honorees will receive their awards Tuesday Eve at 7:30 pm at the Hyatt. Tickets for this meeting event are $55.00 and should be purchased in advance as ACS Meeting Event #117. For those who wish to to attend only the free reception, it starts at 6:30 pm at the Hyatt. ACS Computers in Chemistry Award Symposium Honoring Prof. W. Clark Still Tuesday Morning. 8:25 -- Introductory Remarks. A. ROSSI, T. H. PIERCE 8:30 -- 20. Exploration of Designing Molecules Automatically. W. T. WIPKE, M. Pitman, R. Koehler, M. Kappler 9:05 -- 21. Recent Developments in Molecular Mechanics. N. L. ALLINGER 9:40 -- 22. Organic Reactions and Interactions in Solution. W. L. JORGENSEN 10:15 -- 23. Theoretical Modeling of Stereoselectivities of Diels-Alder Cycloadditions. K. N. HOUK 10:50 -- 24. The Growth of Computational Chemistry in the Pharmaceutical Industry. P. GUND 11:15 -- 25. Award Address-ACS Award for Computers in Chemistry sponsored by Digital Equipment Corporation. Molecular Modeling and Experimental Organic Chemistry. W. C. STILL, J. MACNEILLE, D. CHODOSH -- Sincerely, Thomas Pierce, thpierce@rohmhaas.com or rs0thp@rohvm1 Observation - Network Computing is Computer Slavery. Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From aditya!raman@uunet.UU.NET Sat Feb 13 05:36:19 1993 Date: Sat, 13 Feb 93 13:36:19 -0800 From: aditya!raman@uunet.UU.NET (K. Ramnarayan) Message-Id: <9302132136.AA16855@aditya> To: uunet!ccl.net!chemistry@uunet.UU.NET Subject: FRODO Installation on SGI INDIGO XS24 Hello netters, I am trying to compile Frodo on an SGI indigo XS24. I am getting the following error during compilation: libmld: Internal: st_psym_ifd_isym: ifd (0) or isym (2) out of range. The programs compiles well on an IRIS 4D/320. Any leads as to what may be going wrong. I would very much appreciate your help. Many thanks. .raman From mail Fri Feb 12 15:44:34 1993 Message-Id: <199302122044.AA06687@oscsunb.ccl.net> Date: Fri, 12 Feb 93 15:38:21 EST From: R2VJV%AKRONVM.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: X Windows for PC .. To: chemistry@ccl.net hi, I know that this subject was discussed before in this forum, but i dont have any hardcopy information with me right now. We have a 486 machine and a IBM -R S6000. We have ethernet card on the PC also. We would like the PC to 'talk' to the RS6000 in the X windows environment. I have few names of the commercial ve ndors whose software could simulataneously run X, MS-DOs and MS windows applica tions. Is there any other 'free' software available from ftp sources??? Any inp ut on this subject is appreciated. Thanks in advance. venkat From vazquez@iqm.unicamp.br Fri Feb 12 21:55:17 1993 From: Pedro A.M. Vazquez Message-Id: <9302130055.AA08352@pilsen.iqm.unicamp.br> Subject: X Windows for PC .. To: CHEMISTRY@ccl.net Date: Fri, 12 Feb 93 21:55:17 GMT-3:00 > From: R2VJV%AKRONVM.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU > To: Multiple recipients of list > Subject: X Windows for PC .. > > hi, > I know that this subject was discussed before in this forum, but i dont have > any hardcopy information with me right now. We have a 486 machine and a IBM -R > S6000. We have ethernet card on the PC also. We would like the PC to 'talk' to > the RS6000 in the X windows environment. I have few names of the commercial ve > ndors whose software could simulataneously run X, MS-DOs and MS windows applica > tions. Is there any other 'free' software available from ftp sources??? Any inp > ut on this subject is appreciated. Thanks in advance. > venkat > > Hello: I don't know of any free X software for DOS but I'd like to sugest you 386BSD0.1 from Bill Jolitz. With a SVGA card, an apropriate monitor you can display 1024x768 8bit color pictures at a reasonable speed. 386bsd has full network support (ftp/telnet/nfs/mail), has a very stable X11r5 server and a very good port of Sun's XView3.0 with OpenLook Window Manager (I ported ORTEP to it). It's available from most "big" ftp sites ( the "official" home is agate.berkeley.edu) for free. Regards, Pedro From ikob@les.pc.uec.ac.jp Sat Feb 13 21:21:47 1993 Message-Id: <9302130321.AA18132@les.pc.uec.ac.jp> To: CHEMISTRY@ccl.net Subject: Re: X Windows for PC .. Date: Sat, 13 Feb 93 12:21:47 +0900 From: Katushi Kobayashi Hi, > Hello: > I don't know of any free X software for DOS but I'd like to sugest > you 386BSD0.1 from Bill Jolitz. With a SVGA card, an apropriate monitor > you can display 1024x768 8bit color pictures at a reasonable speed. 386bsd > has full network support (ftp/telnet/nfs/mail), has a very stable X11r5 > server and a very good port of Sun's XView3.0 with OpenLook Window Manager (I > ported ORTEP to it). > It's available from most "big" ftp sites ( the "official" home > is agate.berkeley.edu) for free. > The Linux is an an another UNIX system on PC, you can ftp from major ftp sites (e.g. tsx-11.mit.edu). The Linus distribution packege includes "binary" X11 server. ikob@mor.pc.uec.ac.JP