From chemistry-request@server.ccl.net Mon Jun 26 00:55:33 2000 Received: from hawk.prod.itd.earthlink.net (hawk.prod.itd.earthlink.net [207.217.120.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA07891 for ; Mon, 26 Jun 2000 00:55:33 -0400 Received: from piglet (dialup-63.208.69.74.Chicago1.Level3.net [63.208.69.74]) by hawk.prod.itd.earthlink.net (8.9.3-EL_1_3/8.9.3) with SMTP id VAA05117; Sun, 25 Jun 2000 21:55:16 -0700 (PDT) From: "Slawomir Z. Janicki" To: "GAMESS Users" , "CCL" Subject: NBBP and 3-center bonds Date: Sun, 25 Jun 2000 23:52:34 -0500 Message-ID: <000401bfdf2a$57fad4e0$4a45d03f@piglet> The Natural Bond-Bond Polarizability analysis dies when 3-center bonds are present. Is it a problem with the NBBP definition, or am I missing something obvious? I use PC-GAMESS v. 6.0 with NBO v. 4.M. Also, the Steric analysis dies in every job I try to run. How can I get it to work? Slawomir Janicki janicki1@earthlink.net From chemistry-request@server.ccl.net Mon Jun 26 08:36:12 2000 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA10562 for ; Mon, 26 Jun 2000 08:36:12 -0400 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer); Mon, 26 Jun 2000 13:35:25 +0100 From: uccatvm Message-Id: <8055.200006261235@socrates-a.ucl.ac.uk> Subject: Re: QM/MM codes To: chemistry@ccl.net Date: Mon, 26 Jun 2000 13:35:52 +0100 (BST) In-Reply-To: <200006231512.PAA06965@pc142.iq.ufrj.br> from "Emerson Lima" at Jun 26, 2000 12:34:00 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Emerson, > I'm searchig for molecular modeling programs that performance > conjugate QM/MM calculations. Free softwares are specially wellcome. Could > you suggest me some of these programs? Thank you: A number of computational chemistry packages can do QM/MM simulations: Gaussian (www.gaussian.com) and NWChem (www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html) for example. NWChem is free, but you need to sign a user agreement form, check the NWChem home page. Also the latest version of GAMESS-UK (http://www.dl.ac.uk/CFS) has an interface to the CHARMM QM/MM code. HTH, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)207-679-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Mon Jun 26 09:19:26 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA10743 for ; Mon, 26 Jun 2000 09:19:25 -0400 Received: from voxopm.csc.fi (voxopm.csc.fi [128.214.248.23]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id QAA05785 for ; Mon, 26 Jun 2000 16:19:13 +0300 Date: Mon, 26 Jun 2000 16:19:12 +0300 From: =?ISO-8859-1?Q?Tommi_Nyr=F6nen?= To: CHEMISTRY@ccl.net Subject: Exported PDB files Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Is there a program/pdb parser that can read in a set of plain xyz coordinates of a protein in some format and then write a (pdb) file with the secondary structure information fields (HELIX, SHEET)? Majority of the programs do generate the secondary structure from the coordinates, but do not include this information in the output. We are trying to import structural data into a "non-chemical" visualization program, and would like to have secondary structure information in the input file. All advices/comments are greatly appreciated. Thanks in advance, | Tommi Nyronen CSC Scientific Computing ltd. | Bioinformatics Tekniikantie 15 a D | +358-50-381 9511 P.O.BOX 405 FIN-02101 ESPOO