From chemistry-request@ccl.net Fri Aug 27 08:43:14 2004 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7RDhBa1010582 for ; Fri, 27 Aug 2004 08:43:12 -0500 Received: from caracas-1874.adsl.interware.hu ([213.178.107.82] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.34 #1 (Debian)) id 1C0h99-0008WU-ND; Fri, 27 Aug 2004 15:52:03 +0200 Message-ID: <003701c48c45$d220bf10$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: "boris gorelik" , References: Subject: Re: CCL: Converting cartesian gradients to Z-matrix gradients Date: Fri, 27 Aug 2004 15:54:56 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1,MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Mol2Mol can convert to/from a variety of Z-matrix formats. There are several predefined formats, moreover, as it supports the use of user defined input/output format strings, virtually any kind of Z-matrix or Cartesion formats can be converted. For example a Fenske-Hall type Z-matrix may look like this: ---------------------- some data some data 1 C 0 0.000 0 0.000 0 0.000 2 C 1 1.413 0 0.000 0 0.000 3 C 2 1.400 1 118.931 0 0.000 4 C 3 1.406 2 121.024 1 -1.000 5 C 3 1.101 2 119.066 1 177.200 ..... ------------------------ The corresponding input format string in Mol2Mol is 2 d e u k v l w m which means: skip the first two lines, then the columns contain: dummy data, element symbol, 1st defining atom, distance, 2nd def. atom, angle, 3rd def atom, dihedral. Any combinations are allowed. When writing a Z-matrix, a similar format string (resembling to C format strings) can be defined to produce any kind of Z-matrices. Look at: http://web.interware.hu/frenzy/mol2mol/ Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- From: "boris gorelik" To: "john" Cc: Sent: Thursday, August 26, 2004 7:58 AM Subject: CCL:Converting cartesian gradients to Z-matrix gradients > > > > On Wed, 25 Aug 2004, john wrote: > > > Folks, > > > > I am looking convert a set of cartesian gradients into internal > > gradients in a Z-matrix format. I do have the Z-matrix form of the > > corresponding cartesian coordinates.. > > openbabel can convert between lots of formatst (pdb, mol2, xyz, etc etc). > one of the supported output format is fh, which is Fenske-Hall ZMatrix > file (which holds the internal coordinates of the molecule). Unfortunately > it does not convert into opposite direction. > I have some functions (C++) that convert between internal and cortesian > coordinates. Contact me off the list if you want them > > > > > > > Any suggesstions as to where some code to do this would be most > > appreciated. > > > > Many thanks for your suggestions! > > > > John McKelvey > > > > > > > > > > > > Jan Labanowski,jlabanow$at$nd.edu (read about it on CCL Home Page) > > > > > > > > > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >