From chemistry-request@server.ccl.net Mon Jan 1 06:58:33 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23328 for ; Mon, 1 Jan 2001 06:58:33 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id MAA09781 for ; Mon, 1 Jan 2001 12:58:22 +0100 (MET) Date: Mon, 1 Jan 2001 12:58:22 +0100 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CDA & Turbomole Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Happy New Year, to everybody at first. I was wondering whether someone has modified the CDA program of Frenkings group to use it with Turbomole rather than with Gaussian. Any pointer is highly appreciated. Peter ---------------------------------------------- Peter Burger Anorg.-chem. Institut University of Zuerich From chemistry-request@server.ccl.net Mon Jan 1 13:14:35 2001 Received: from mail2.organik.uni-erlangen.de (lesath.chemie.uni-erlangen.de [131.188.127.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24528 for ; Mon, 1 Jan 2001 13:14:35 -0500 Received: from ccc.chemie.uni-erlangen.de (wtewael [131.188.127.223]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id TAA13121; Mon, 1 Jan 2001 19:14:18 +0100 (MET) Sender: Wolf-Dietrich.Ihlenfeldt@ccc.chemie.uni-erlangen.de Message-ID: <3A50C8F9.6DF04637@ccc.chemie.uni-erlangen.de> Date: Mon, 01 Jan 2001 19:14:17 +0100 From: Wolf-Dietrich Ihlenfeldt Organization: Computer Chemistry Center X-Mailer: Mozilla 4.7 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Asim Kumar Debnath CC: chemistry@ccl.net Subject: Re: CCL:file convertion References: <3A4CB44C.894DE05F@nybc.org> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Asim Kumar Debnath wrote: > > Hi! > I would greatly appreciate if someone can give me suggestions on > how to convert a pdb file [containing multiple small molecules that > was obtained from DOCK (UCSF) run] to a mult-mol2 or multi-sdf file. You mean a 'multi-record SD-file', I presume? One structure per record? > I would also like to keep the mol-ID of each compound in those files. > Thank you in advance for your help and Happy New Year to all of > you! > > Asim > You problem can be solved by a small application script. Please download the latest release of the CACTVS toolkit for your platform from our ftp server (ftp://www2.ccc.uni-erlangen.de/pub/cactvs) and install the standard toolkit (unpack in empty, temporary directory, execute the 'installme' script and answer its questions). Next store the following script in a text file (named for example 'convertpdb.tcl'): --- foreach file $argv { if {[catch {molfile open $file} fh]} { puts stderr $fh } else { if {[catch {molfile read $fh} eh]} { puts stderr $eh } else { set fh2 [molfile open [file rootname $file].sdf w] foreach eh2 [ens split $eh] { molfile write $fh2 $eh2 ens delete $eh2 } molfile close $fh2 } molfile close $fh } } --- Finally run this script as: csts -f convertpdb.tcl file1.pdb file2.pdb... Other formats and processing of the structures before they are written out (such as djusting hdyrogens) can easily be added by means of additional script commands. Since I do not know how the MolID is stored in your PDB file, this script will probably not yet preserve it. If you can provide me with a sample PDB file, I will send you an updated script which does have this feature. The software is free for educational and non-profit use. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/