From owner-chemistry@ccl.net Mon Jul 18 07:09:14 2005 From: "CCL" To: CCL Subject: CCL: LANL2DZ in G03 Message-Id: <-28901-050718055148-24924-eSc6C2yCCSce8pLLLmWjCA(-)server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Pierre Archirel Dear collegues, 1- in the first case (PtCl2O) the keyword "pseudo=read" expects a specific card to be given. After the end of basis (****) give a blank line and the data lines for the pseudo: Pt 0 lanl2dz blankline 2- in the second case (Zn...) this keyword "pseudo=read" must be given and also the data after the basis: Zn 0 lanl2dz blankline The "strange" geometries are due to the lack of pseudo. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel(-)lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Mon Jul 18 12:26:24 2005 From: "CCL" To: CCL Subject: CCL: Drawing in Linux Message-Id: <-28902-050716131320-32541-eSc6C2yCCSce8pLLLmWjCA(_)server.ccl.net> X-Original-From: "Felipe Fleming" Content-Type: multipart/alternative; boundary="----=_NextPart_000_003E_01C58A08.C5FC1290" MIME-Version: 1.0 Sent to CCL by: "Felipe Fleming" This is a multi-part message in MIME format. ------=_NextPart_000_003E_01C58A08.C5FC1290 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello! I was wondering if anyone would know a program like ChemDraw for = Linux? Thank you all in advance, Fleming ------=_NextPart_000_003E_01C58A08.C5FC1290 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello! I was wondering if anyone would = know a=20 program like ChemDraw for Linux?

Thank you all in advance,

Fleming

------=_NextPart_000_003E_01C58A08.C5FC1290-- From owner-chemistry@ccl.net Mon Jul 18 15:00:27 2005 From: "CCL" To: CCL Subject: CCL: W:Using Antechamber with Gamess and other molecular manipulations Message-Id: <-28903-050718145714-29547-eSc6C2yCCSce8pLLLmWjCA[*]server.ccl.net> X-Original-From: "Charles Karney" Sent to CCL by: "Charles Karney" Dear Colleagues: I'd like to announce the availability of some scripts for manipulating molecules written by researchers at Sarnoff Corporation under the Engineered Identification and Countermeasures Program which is funded by the U.S. Army Medical Research and Materiel Command under Contract No. DAMD17-03-C-0082. The main objectives of these scripts are * Allow Gamess to be used in conjunction with Antechamber for the assignment of partial charges by the RESP or AM1-BCC methods. * Add hydrogens to a PDB file using Gromacs and adjust atom names and certain bond angles to conform to Amber's rules. A couple of shortcomings of Antechamber are addressed. * The charges produced by the AM1-BCC method are symmetrized between chemically equivalent atoms (using respgen's symmetry detection). * Antechamber produces several temporary files which mean that it is unsafe to run multiple instances within the same directory. This is addressed by placing the temporary files in a unique directory. A full description of the scripts and the scripts themselves can be found at http://www.sarnoff.com/products_services/government_solutions/epic/scripts.asp A backup site is http://charles.karney.info/b2d-scripts/index.html Questions, comments, and improvements on this work should be sent to ckarney[*]sarnoff.com -- Charles Karney Sarnoff Corporation, Princeton, NJ 08543-5300 URL: http://charles.karney.info Tel: +1 609 734 2312 Fax: +1 609 734 2323