From chemistry-request@ccl.net Sun Apr 24 00:47:07 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.201]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3O4l3SP009002 for ; Sun, 24 Apr 2005 00:47:04 -0400 Received: by rproxy.gmail.com with SMTP id r35so821480rna for ; Sat, 23 Apr 2005 21:47:02 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=iYIyFMAC2Y6MoPrZpaTwfH9+ddqMXO2T8HQEXSBgVK2Up53zcNf7pJ2qjrnVnXG28wXt/auIbB1VFEKGtjCpEG/ATAWTTvDHkUXYnn9XN3AJzIg2kIwEU4XO9tnonrUH50FbjKuMOm6wWVYWa/MOhC+YJICu6GyzyECoE4zDhkE= Received: by 10.38.125.45 with SMTP id x45mr5156284rnc; Sat, 23 Apr 2005 21:47:02 -0700 (PDT) Received: by 10.38.86.50 with HTTP; Sat, 23 Apr 2005 21:47:02 -0700 (PDT) Message-ID: Date: Sat, 23 Apr 2005 23:47:02 -0500 From: sunnylele Reply-To: sunnylele To: chemistry #%# ccl.net Subject: CCL:some advise on how to optimize the MeOH when fixing O-H >=6 A using G03? Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j3O4l7SP009028 Hi, I just want to test the method with this trival structure. when the O-H distance is fixed >=6 A, wavefunction is too hard to converge, so optimization becomes impossible. Now the best possible level is ub3lyp/6-31++G*, when the SCF can converge twice. However, it is not enough for optimizaiton. Thanks, Jing From chemistry-request@ccl.net Sun Apr 24 11:47:06 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3OFkvh0001830 for ; Sun, 24 Apr 2005 11:46:59 -0400 Received: from 9.171-182-adsl-pool.axelero.hu ([81.182.171.9] helo=[192.168.0.25]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1DPjJv-0008OS-5B TLS Cipher TLSv1:AES256-SHA:256; Sun, 24 Apr 2005 17:46:56 +0200 Message-ID: <426BBE84.8070200 (a) chemaxon.com> Date: Sun, 24 Apr 2005 17:43:00 +0200 From: Szabolcs Csepregi Organization: Chemaxon Ltd. User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Sean, , OBrien" CC: chemistry (a) ccl.net Subject: Re: CCL:W:Substructure matching References: <200504222302.j3MN28ee024016 (a) server.ccl.net> In-Reply-To: <200504222302.j3MN28ee024016 (a) server.ccl.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi Sean, You can do this easily in Java using the MolSearch class of the JChem API. See documentation including example: http://www.jchem.com/doc/api/chemaxon/sss/search/MolSearch.html We also have a command-line program called jcsearch: $ jcsearch --allHits -q 'c1cncn1' 'C1CCC(CC1)c2c[nH]cn2' Query has 1 match: Match 1:[ 7, 8, 9, 10, 11 ] C1CCC(CC1)c2c[nH]cn2 $ jcsearch --allHits --orderSensitive -q 'c1cncn1' 'C1CCC(CC1)c2c[nH]cn2' Query has 2 matches: Match 1:[ 7, 8, 9, 10, 11 ] Match 2:[ 8, 7, 11, 10, 9 ] C1CCC(CC1)c2c[nH]cn2 http://www.jchem.com/doc/user/Jcsearch.html JChem is free for academia, see: http://www.chemaxon.hu/forum/ftopic193.html All the best, Szabolcs Sean, , OBrien wrote: > Hi All, > > I am searching for some software that will help me to identify > the atoms within a molecule that match a query substructure. > For example I wish to find which atoms belong to an imidazole > ring. The aim is to extract the matching substructure while > keeping the original atomic coordinates. > > I know that several substructure matching routines exist, and > some are even freely available but I haven't found any that > return the identity of the matching atoms. Some return the > whole molecule or a tally of how many times the substructure > is present. They obviously "know" which atoms match but I am > having difficulty identifying them. Similarly matching strings > in SMILES doesn't return the initial atom ids. > > I would be very grateful for any routines that do this, or that > can be modified for this purpose, > > Many Thanks, > > Sean O'Brien > > > -= 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 (a) ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST (a) ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Szabolcs Csepregi, PhD ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3620 4219863 Tel: +361 4532661 Fax: +361 4532659 mailto:scsepregi (a) chemaxon.com