From chemistry-request- at -server.ccl.net Sat May 18 15:01:34 2002 Received: from addu.axelero.hu ([195.228.240.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4IJ1Td04688 for ; Sat, 18 May 2002 15:01:33 -0400 Received: from cthulhu (line-141-237.dial.matav.net [145.236.141.237]) by mail02.axelero.hu (iPlanet Messaging Server 5.1 (built Jan 30 2002)) with SMTP id <0GWB003HXM6FAJ-!at!-mail02.axelero.hu> for chemistry-!at!-ccl.net; Sat, 18 May 2002 21:01:28 +0200 (MEST) Date: Sat, 18 May 2002 21:03:21 +0200 From: "Tamas E. Gunda" Subject: Re: CCL:Ligand preparation To: amor san juan , chemistry |-at-| ccl.net Message-id: <007101c1fe9e$adfe0c00$0200a8c0 -A_T- cthulhu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <1021360120.3ce0b7f8a9c1b \\at// mail.up.edu.ph> The file you produced this way is a 2D drawing. Therefore addition of hydrogens and any further manipulations are nonsense. You should use a real modelling application. Tamas ----- Original Message ----- From: "amor san juan" To: Sent: Tuesday, May 14, 2002 9:08 AM Subject: CCL:Ligand preparation > Dear AutoDocker's community: > > Can someone recommend any other softwares for ligand preparation (aside > from > chemskestch5, babel &/or ADT). I need your help. > > Using Chemsketch5 I draw the benzamidine(ben.mol) structure then, used Babel to > add explicit hydrogens & ben.mol2 conversion. The result is flawed ben.pdbq > file as viwed below: > > REMARK 2 active torsions (identified by new id numbers): > REMARK status: ('A' for Active; 'I' for Inactive) > REMARK I 3- 7 between atoms: C3 and C7 > REMARK 1 A 7- 8 between atoms: C7 and N1 > REMARK 2 A 7- 10 between atoms: C7 and N2 > ROOT > ATOM 1 A1 <1> 1 -4.129 2.188 0.000 0.00 0.00 0.000 2 > ATOM 2 A2 <1> 1 -4.129 1.362 0.000 0.00 0.00 0.000 2 > ATOM 3 A3 <1> 1 -3.417 0.954 0.000 0.00 0.00 0.000 3 > ATOM 4 A4 <1> 1 -2.705 1.362 0.000 0.00 0.00 0.000 2 > ATOM 5 A5 <1> 1 -2.705 2.188 0.000 0.00 0.00 0.000 2 > ATOM 6 A6 <1> 1 -3.417 2.604 0.000 0.00 0.00 0.000 2 > ATOM 7 C7 <1> 1 -3.417 0.129 0.000 0.00 0.00 0.000 3 > ENDROOT > BRANCH 7 8 > ATOM 8 N1 <1> 1 -4.132 -0.283 0.000 0.00 0.00 0.000 2 > ATOM 9 H6 <1> 1 -5.107 -0.581 0.000 0.00 0.00 0.000 1 > ENDBRANCH 7 8 > BRANCH 7 10 ATOM 10 > N2 <1> 1 -2.703 -0.283 0.000 0.00 0.00 0.000 3 > ATOM 11 H7 <1> 1 -2.703 -1.303 0.000 0.00 0.00 0.000 1 > ATOM 12 H8 <1> 1 -1.819 0.227 0.000 0.00 0.00 0.000 1 > ENDBRANCH 7 10 > TDOF 3 > > ------------------ > Diagramatically, the steps I did to prepare ligand is: > > ben.mol -----> ben.mol2 ---------> ben.pdbq > babel autotors3 > > Alternatively, I used ADT yet, the same zeros in last columns appeared (no > charge present). > > Amor > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY -A_T- ccl.net -- To Everybody | CHEMISTRY-REQUEST -A_T- ccl.net -- To Admins > MAILSERV /at\ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH ":at:" ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl[ AT ]ccl.net > > > > > >