From chemistry-request&$at$&server.ccl.net Tue May 14 03:02:43 2002 Received: from web2.up.edu.ph ([64.94.101.194]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4E72dg29032 for ; Tue, 14 May 2002 03:02:39 -0400 Received: (qmail 22955 invoked by uid 504); 14 May 2002 07:25:13 -0000 Received: from amor_sanjuan -x- at -x- yahoo.com by web2 with qmail-scanner-1.01 (update: v4202 08 May 2002. Clean. Processed in 0.403989 secs); 14 May 2002 07:25:13 -0000 Received: from unknown (HELO b01.mail.up.edu.ph) (10.16.3.1) by 10.16.3.144 with SMTP; 14 May 2002 07:25:12 -0000 Received: (qmail 19766 invoked from network); 14 May 2002 07:05:26 -0000 Received: from unknown (HELO localhost) ([10.16.3.5]) (envelope-sender ) by 10.16.3.1 (qmail-ldap-1.03) with SMTP for ; 14 May 2002 07:05:26 -0000 Received: from 10.32.129.44 ( [10.32.129.44]) as user aasanjuan {*at*} b03.mail.up.edu.ph by mail.up.edu.ph with HTTP; Tue, 14 May 2002 15:08:40 +0800 Message-ID: <1021360120.3ce0b7f8a9c1b $#at#$ mail.up.edu.ph> Date: Tue, 14 May 2002 15:08:40 +0800 From: amor san juan To: chemistry _-at-_)ccl.net Subject: Ligand preparation MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 10.32.129.44 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