From owner-chemistry@ccl.net Fri Jul 14 09:26:01 2006 From: "John McKelvey jmmckel::attglobal.net" To: CCL Subject: CCL: Gaussian based dipole moment matrix element code Message-Id: <-32135-060714072849-16876-ePdMJ6Pkgn9OWEC2krDTxQ#%#server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Jul 2006 07:18:19 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel^-^attglobal.net] CCLers, I would like to include a full dipole moment matrix element procedure in a code. Any suggestions where I could find such? Thanks! John McKelvey From owner-chemistry@ccl.net Fri Jul 14 11:29:01 2006 From: "Prabha Jayapal prabha.jayapal++gmail.com" To: CCL Subject: CCL: gibbs- bond constraint Message-Id: <-32136-060713074248-29411-/sJF2B0kYRkqBwnBe+4mmQ[]server.ccl.net> X-Original-From: "Prabha Jayapal" Content-Type: multipart/alternative; boundary="----=_Part_10511_25998404.1152788577815" Date: Thu, 13 Jul 2006 12:02:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Prabha Jayapal" [prabha.jayapal**gmail.com] ------=_Part_10511_25998404.1152788577815 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCl members; I am new to molecular dynamics calculations. I want to carry on MD run with bond constraint. I am using amber 7. Could anybody help me with an example input format (gibin) for using gibbs module? Thanks in advance. regards J.Prabha -- Prabha Jayapal, Department of Cemistry, University of Manchester, Oxford road,Manchester-M13 9pl Uk ------=_Part_10511_25998404.1152788577815 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
 Dear CCl members;
           I am new to molecular dynamics calculations. I want to carry on MD run with bond constraint. I am using amber 7. Could anybody help me with an example input format (gibin) for using gibbs module?  Thanks in advance.
 
regards
J.Prabha 

--
Prabha Jayapal,
Department of Cemistry,
University of Manchester,
Oxford road,Manchester-M13 9pl
Uk
 
------=_Part_10511_25998404.1152788577815-- From owner-chemistry@ccl.net Fri Jul 14 12:04:01 2006 From: "John McKelvey jmmckel~!~attglobal.net" To: CCL Subject: CCL: Ancient HONDO Code Message-Id: <-32137-060714114612-24367-7XQA3kyJJ6E/9caoklREpQ- -server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Jul 2006 11:36:01 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[A]attglobal.net] Hello! Several decades ago while Michel Dupuis was still a grad student at Buffalo and I was at Kodak I beta tested HONDO for QCPE... Would anyone still have such a /really old/ source version for HONDO? Cheers, John McKelvey From owner-chemistry@ccl.net Fri Jul 14 15:28:00 2006 From: "Jeff Hammond jhammond .. uchicago.edu" To: CCL Subject: CCL:G: Gaussian based dipole moment matrix element code Message-Id: <-32138-060714133109-6091-nAxgjRwRFgqwAVWT8rYd0Q^-^server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Jul 2006 09:40:26 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jhammond*uchicago.edu] You can do this in GAMESS (free), NWChem (free) and Gaussian ($$$) as well as open source (available on SourceForge) codes. GAMESS is probably the most widely used package for this kind of thing. In GAMESS, you would modify less than 10 lines in the source code to print the dipole integrals. A colleague of mine did this so I could send you the code changes if necessary. In NWChem, there is a dipole integral module you can find and add a print statement appropriately. Because NWChem code doesn't "feel" like old-school Fortran, it might take longer to figure out the modifications. However, NWChem's property integrals are based on Hondo, which you appear to have an affinity for. Although I don't have access to Gaussian source code, Z. Zhao, et al. acknowledge Doug Fox and Jim Hess at Gaussian for technical support, which I assume included printing out dipole integrals, in "The Reduced Density Matrix Method for Electronic Structure Calculations and the Role of Three-Index Representability" (The Journal of Chemical Physics, 2004). Tonto (http://www.theochem.uwa.edu.au/tonto) and PyQuante (http://pyquante.sourceforge.net) are open source packages which should be very easy to program in. While the may not have dipole routines now, adding them would be very easy. Jeff John McKelvey jmmckel::attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel^-^attglobal.net] > CCLers, > > I would like to include a full dipole moment matrix element procedure in > a code. Any suggestions where I could find such? > > Thanks! > > John McKelvey From owner-chemistry@ccl.net Fri Jul 14 16:03:00 2006 From: "Jason Thompson Thompson.Jason1++mayo.edu" To: CCL Subject: CCL: Ancient HONDO Code Message-Id: <-32139-060714152034-24793-km303LqBg1qDl4RpfoLNJQ]_[server.ccl.net> X-Original-From: Jason Thompson Content-Type: multipart/alternative; boundary=Apple-Mail-14-649147475 Date: Fri, 14 Jul 2006 13:42:02 -0500 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Jason Thompson [Thompson.Jason1-$-mayo.edu] --Apple-Mail-14-649147475 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Not exactly ancient (I believe HONDOPLUS is based on HONDO 99.6): http://comp.chem.umn.edu/hondoplus/ You could e-mail the software manager (see bottom of above the HONDOPLUS web page) for possible older versions they may have laying around. On Jul 14, 2006, at 12:44 PM, John McKelvey jmmckel~!~attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel[A]attglobal.net] > Hello! > > Several decades ago while Michel Dupuis was still a grad student at > Buffalo and I was at Kodak I beta tested HONDO for QCPE... Would > anyone still have such a /really old/ source version for HONDO? > > Cheers, > > John McKelvey > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > Jason D. Thompson, Ph.D. Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Guggenheim 6-93 200 First Street SW Rochester, MN 55905 (507)-284-1758 http://pollux.chem.umn.edu/~thompson --Apple-Mail-14-649147475 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Not exactly ancient (I believe = HONDOPLUS is based on HONDO 99.6):


You = could e-mail the software manager (see bottom of above the HONDOPLUS web = page) for possible older versions they may have laying = around.

On Jul 14, 2006, at 12:44 PM, John = McKelvey jmmckel~!~attglobal.net wrote:

Sent to CCL by: John McKelvey = [jmmckel[A]attglobal.net]

Several decades ago while Michel Dupuis was still a = grad student at=A0
Buffalo and I was at Kodak I beta tested HONDO for = QCPE... =A0 Would=A0
anyone = still have such a /really old/ source version for HONDO?


John McKelvey



-=3D = This is automatically added to each message by the mailing script = =3D-
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If your mail bounces from CCL with 5.7.1 error, = check:



=

Jason D. Thompson, Ph.D.

Molecular Pharmacology and Experimental = Therapeutics

Mayo Clinic

Guggenheim 6-93

200 First Street SW

Rochester, MN 55905

(507)-284-1758

http://pollux.chem.umn.edu/~= thompson


= --Apple-Mail-14-649147475-- From owner-chemistry@ccl.net Fri Jul 14 23:50:00 2006 From: "Scott Dixon scott!A!metaphorics.com" To: CCL Subject: CCL: generating SMIRKS files Message-Id: <-32140-060714130816-31131-jrc0JFWPYAZmSvtDwOOhCA]-[server.ccl.net> X-Original-From: Scott Dixon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 14 Jul 2006 09:08:48 -0700 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Scott Dixon [scott#,#metaphorics.com] The next release of the Daylight software will have a conversion tool which will convert between rxn MOL files and Daylight SMIRKS. The current release will do conversions from MOL files to SMILES and from rxn MOL files to reaction SMARTS. Academic licenses are available. For further information and contacts go to http://www.daylight.com Scott Dixon Daylight CIS On Jul 10, 2006, at 6:19 PM, Didier Rognan didier.rognan*pharma.u- strasbg.fr wrote: > Sent to CCL by: Didier Rognan [didier.rognan:-:pharma.u-strasbg.fr] > Dear colleagues, > > > Has anyone a free routine able to convert a MDL rxn file into SMIRKS ? > > > Many thanks for your answer > > Kind regards > ---------------------------------------------------------------------- > ------------------------- > Dr. Didier ROGNAN > Directeur de Recherche > CNRS UMR 7175-LC1 > Institut Gilbert-Laustriat > 74, route du Rhin, B.P.24 > F-67401 Illkirch > > direct line: +33 (0)3 90 24 42 35 > secretary: +33(0)3 90 24 42 20 > fax: +33 (0)3 90 24 43 10 > email: didier.rognan]-[pharma.u-strasbg.fr > www:http://bioinfo-pharma.u-strasbg.fr > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > >