From owner-chemistry@ccl.net Wed Aug 24 07:55:39 2005 From: "CCL" To: CCL Subject: CCL: Phenoxycarbonyl Radical Message-Id: <-28990-050824074506-16109-sJTYeKniThUXNerGpwThRw : server.ccl.net> X-Original-From: "Jens Spanget-Larsen" Sent to CCL by: "Jens Spanget-Larsen" Dear CCL, I am looking for information on the "phenoxycarbonyl radical", Ph-O-C'=O (formal radical center on the primed carbon, C'). Are you aware of any theoretical or experimental investigations? Yours, Jens >--< >---------------------------------------------------------< JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget : ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget >---------------------------------------------------------< From owner-chemistry@ccl.net Wed Aug 24 08:23:13 2005 From: "CCL" To: CCL Subject: CCL: W:Re: CCL: parameters for Al in GAMESS+Tinker Message-Id: <-28991-050824080415-20416-sJTYeKniThUXNerGpwThRw-,-server.ccl.net> X-Original-From: "Nicolas Ferre" Sent to CCL by: "Nicolas Ferre" Hi, it looks like you forget to add a atom type number to your Al atoms: 0 is not valid. What number did you choose in your modified mm2 parameters file ? It should be more than 75. > Sent to CCL by: "Baltrusaitis, Jonas" > Hello, > > while trying to proceed with geometry optimization using Al atoms containing cluster with GAMESS+Tinker code MM/QM procedure I get error message: > > Undefined or Illegal Atom Types : > > and all my Al atoms are marked as undefined. I built a custom parameter set from literature references using text editor, but it looks like Tinker doesn't recognize it as valid. I nitially it gave same error when I tried to use mm2 parameter file, but the new one definetile has Al atoms in it. What can be wrong? > Here is one instance of your error: 0 between the coordinates and the connectivity is wrong. > > INPUT CARD> 2 AL -2.381000 4.124000 4.548000 0 14 13 10 Hope this helps, Nicolas -- *********** Dr. Nicolas Ferre' *********** Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universites Aix-Marseille Case 521 Centre de Saint-Jerome 13397 - Marseille Cedex 20, France Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 http://www.up.univ-mrs.fr/cbrl/lctmm ************************************************************** From owner-chemistry@ccl.net Wed Aug 24 17:07:52 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-28992-050824170649-14341-sJTYeKniThUXNerGpwThRw!A!server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Lins?= Content-Type: multipart/alternative; boundary="----=_Part_473_3167924.1124917605574" Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Lins?= ------=_Part_473_3167924.1124917605574 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi all! I want to run a MD calculation of water molecules on a gold surface using= =20 2D periodic boundary conditions. Does anobody knows a program that can do= =20 it, painless? Thanks in advance. --=20 ---- Jo=E3o Ot=E1vio M. A. Lins ------=_Part_473_3167924.1124917605574 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
 Hi all!
 
 I want to run a MD calculation of water molecules on a gold surf= ace using 2D periodic boundary conditions. Does anobody knows a program tha= t can do it, painless?
 
 Thanks in advance.

--
----
Jo=E3o Ot= =E1vio M. A. Lins
 
------=_Part_473_3167924.1124917605574-- From owner-chemistry@ccl.net Wed Aug 24 19:56:44 2005 From: "CCL" To: CCL Subject: CCL: Out of the office, RE: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-28993-050824195638-6306-sJTYeKniThUXNerGpwThRw*_*server.ccl.net> X-Original-From: Sun Choi Sent to CCL by: Sun Choi I am on vacation from August 22, and I will be back in office on Tuesday September 06. Thanks, Sun From owner-chemistry@ccl.net Wed Aug 24 20:57:15 2005 From: "CCL" To: CCL Subject: CCL: Out of the office, RE: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-28994-050824185555-3630-sJTYeKniThUXNerGpwThRw|*|server.ccl.net> X-Original-From: Bjoern Loeprecht Sent to CCL by: Bjoern Loeprecht Dear Tripos Customer, I will be out of office till August-29-2005. Please send your email again to desupport|*|tripos.com In case you did that please disregard this email. Sorry for this inconvenience. Best regards, Dr. Bjoern Loeprecht Application Scientist _________________________________________________________ Tripos GmbH * Martin-Kollar-Strasse 17 * D-81829 Muenchen Tel: +49-89-451030-0 * Fax: +49-(0)89-451030-0 Email: desupport|*|tripos.com * Web: http://www.tripos.com From owner-chemistry@ccl.net Wed Aug 24 21:13:43 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-28995-050824194141-5565-sJTYeKniThUXNerGpwThRw.:.server.ccl.net> X-Original-From: Rick Venable Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: Rick Venable On Wed, 24 Aug 2005, CCL wrote: > I want to run a MD calculation of water molecules on a gold surface > using 2D periodic boundary conditions. Does anobody knows a program > that can do it, painless? > Thanks in advance. > ---- > João Otávio M. A. Lins Why not put a gold slab thru the middle, and use standard 3D PBC? You get twice the surface area that way as well. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable.:.nih.gov ALT email: rvenable.:.speakeasy.org ------------------------------------- nekcihC toboR