From owner-chemistry@ccl.net Sat Jan 14 09:01:00 2006 From: "Pradipta Bandyopadhyay pradipta/a\iitg.ernet.in" To: CCL Subject: CCL: code for internal to cartesian! Message-Id: <-30498-060114030259-18208-4QkiKnl5fBkbcGKRXCmRWA(0)server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 14 Jan 2006 11:51:14 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta\a/iitg.ernet.in] Hello, Does anyone have a fortran code for converting cartesian coordiantes to internals (bond, angle, dihedral) and internals to cartesians? thanks Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta*iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Sat Jan 14 09:59:00 2006 From: "Vincent Xianlong Wang xloongw*yahoo.com" To: CCL Subject: CCL:G: internal rotation in hydrocarbons Message-Id: <-30499-060114095700-20659-leDWIcBBsCxz1Ipre6cvIQ:_:server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 14 Jan 2006 06:56:55 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw(!)yahoo.com] Hi Jim, I have Mathematica codes to solve the 1-D Schrodinger equation using three methods: free rotor basis expansion, finite-boundary-condition(I guess this is the grid method you called), and the Mathieu functions. If you need, I can send you the codes along an appendix of my thesis on internal rotation study. Best regards, Vincent --- "Jim Pfaendtner pfaendtner^northwestern.edu" wrote: > Sent to CCL by: "Jim Pfaendtner" > [pfaendtner[-]northwestern.edu] > Hi, > > I am trying to develop a short code which will take > a 1-D relaxed PES scan of my dihedral angles and > allow me to calculate the energy levels from the 1D > schrodinger equation. I'm obtaining the PES as a > full fourier fit from Gaussian simulations. > > Can anyone recommend a good method to obtain the > lowest eigenvalues from the 1D schrodinger equation? > The PES scans are fit to full Fourier series > because because my molecules are somewhat irregular. > > I have been trying to use a grid-based method but > haven't had much luck. If people know of any > public-domain codes which can help me with this, I > would greatly appreciate it. > > Regards, > Jim Pfaendtner > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the !^! > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Jan 14 16:46:00 2006 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jvilla^imim.es" To: CCL Subject: CCL: code for internal to cartesian! Message-Id: <-30500-060114121628-26092-IsfkCl91h8TfjxjPbVaTMg%a%server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 14 Jan 2006 17:29:10 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jvilla(0)imim.es] Dear Pradipta, in Polyrate code we developed some years ago these routines. I am not a developer o the code anymore but you may find it at the web of Don Truhlar's group http://comp.chem.umn.edu/polyrate/ Take care Jordi En/na Pradipta Bandyopadhyay pradipta/aiitg.ernet.in ha escrit: > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta\a/iitg.ernet.in] > Hello, > > Does anyone have a fortran code for converting cartesian coordiantes to > internals (bond, angle, dihedral) and internals to cartesians? > > thanks > > Pradipta > > > Dr. Pradipta Bandyopadhyay > Assistant Professor > Dept. of Biotechnology > Indian Institute of Technology, Guwahati > Phone: 91-361-258-2213 (office) > e-mail: pradipta[-]iitg.ernet.in > web: http://202.141.80.5/~pradipta/Pradipta.htm > > > ----------------------------------------------------------------------------------- > This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. > http://www.iitg.ernet.in> > > > > > -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF C/ Doctor Aiguader, 80; 08003 Barcelona (Spain) Tel: +34 93 221 1009 ext 2619 // Fax: +34 93 221 3237 e-mail: jvilla..imim.es http://diana.imim.es MSc on Bioinformatics for Health Sciences http://diana.imim.es/mbio http://www.idec.upf.edu/mbio From owner-chemistry@ccl.net Sat Jan 14 18:43:00 2006 From: "Robinson, James James.Robinson-.-evotec.com" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30501-060114183818-1026-3bMyOfKH7ok6n7Bjyh5K8g*server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 14 Jan 2006 22:53:33 -0000 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson\a/evotec.com] Not everyone has time and resources to run resource hungry calculations, for instance QCISD(T) or even B3lYP/6-311+(2d,p), sometimes a calculation to simply disprove/support an idea is adequate. The biggest stumbling block is the failure of us all to come up with something quicker than SCF algorithms for ab initio calculations. There are instances when semi-empirical calculations take minutes and provide an adequate qualitative answer. I think Feynmann said if theories don't match experiment scrap the theory..okay which ab initio, DFT, semi-empirical calc satisfies that. Work with the tools you have and some chemistry knowledge. Think; do not accept blindly and do not stick to your own ideas because of vanity. None of the calculations are perfect or ever big enough to mimic reality. Dr J J Robinson, UK. -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net] Sent: 14 January 2006 03:47 To: Robinson, James Subject: CCL: Semiempirical examples for teaching: success stories Sent to CCL by: Terry Frankcombe [T.Frankcombe[]chem.leidenuniv.nl] *cough* *splutter* Sorry James, but that's complete nonsense (to put it politely). Since when have semiempirical extrapolations* been taken over experimental data? Complete codswallop. A lot of the claims you make in that paper are questionable at best. What you have shown are best interpreted as FAILURES of semiempirical and DFT methods, not wins. Terry *I say extrapolations to highlight that semiempirical methods applied outside their training set are not much more than guesses. Informed guesses, but guesses nonetheless. -- Dr Terry Frankcombe LIC / Theoretical Chemistry University of Leiden Postbus 9502, 2300 RA Leiden, The Netherlands Ph. +31 71 527 4533 Fax +31 71 527 4397 > Sent to CCL by: "James J. P. Stewart" [mrmopac||worldnet.att.net] > --=====================_177286794==.ALT > Content-Type: text/plain; charset="us-ascii"; format=flowed > > My apologies: My last message re semiempirical methods contained > invalid URLs