From chemistry-request@server.ccl.net Fri Apr 7 04:28:59 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA11686 for ; Fri, 7 Apr 2000 04:28:58 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA76993 for ; Fri, 7 Apr 2000 10:49:56 +0200 (CEST) Date: Fri, 7 Apr 2000 10:49:56 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: AutoDock parameters for Br, Cl, F In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers, I'm going to dock several inhibitors which are comprised of C, N, H, O, S, but also of Br, Cl, F. When I started to modify the gpf- and dpf-Files to introduce the latter elements I noticed that there are differences in the parameters between those published on the AutoDock- webpage (which were used with AutoDock 2.4) and the parameters employed by the scripts mkgpf3 and mkdpf3 for all elements. Example: parameters for carbon carbon parameters used in mkgpf3 parameters used with AutoDock 2.4 map 1b41_07.C.map C.map nbp_r_eps 4.00 0.0222750 12 6 #C-C lj nbp_r_eps 4.00 0.1500 12 6 #C-C equilibrium separation and well-depth nbp_r_eps 3.75 0.0230026 12 6 #C-N lj nbp_r_eps 3.75 0.1549 12 6 #C-N equilibrium separation and well-depth nbp_r_eps 3.60 0.0257202 12 6 #C-O lj nbp_r_eps 3.60 0.1732 12 6 #C-O equilibrium separation and well-depth nbp_r_eps 4.00 0.0257202 12 6 #C-S lj nbp_r_eps 4.00 0.1732 12 6 #C-S equilibrium separation and well-depth nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0548 12 6 #C-H equilibrium separation and well-depth There is a constant factor 6.734 between the well-depths (3rd cols)of the new parameters compared to the old parameters (12-6-potential). I was unable to find an eplanation for this. Can anybody help me ? Cheers, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de -----------------------------------------------------------------