From kallies@serv.chem.uni-potsdam.de Thu Apr 30 09:27:55 1998 Received: from hp.rz.uni-potsdam.de for kallies@serv.chem.uni-potsdam.de by www.ccl.net (8.8.3/950822.1) id IAA19155; Thu, 30 Apr 1998 08:41:50 -0400 (EDT) Received: from serv.chem.uni-potsdam.de (serv.chem.uni-potsdam.de [141.89.160.2]) by hp.rz.uni-potsdam.de (8.8.8/8.8.8) with SMTP id OAA21970; Thu, 30 Apr 1998 14:41:03 +0200 (MESZ) Received: from pch10.chem.uni-potsdam.de by serv.chem.uni-potsdam.de (AIX 4.1/UCB 5.64/4.03) id AA20030; Thu, 30 Apr 1998 14:30:55 +0100 Message-Id: <35487265.5477AA0F@serv.chem.uni-potsdam.de> Date: Thu, 30 Apr 1998 14:45:25 +0200 From: Bernd Kallies X-Mailer: Mozilla 4.04 [en] (Win95; I) Mime-Version: 1.0 To:chemistry@www.ccl.net Subject: parm94 and glycam93 in AMBER Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are currently dealing with molecular mechanics calculations on proteins coupled with oligosaccharides. We decided to use an AMBER force field together with GLYCAM. The original GLYCAM paper (Woods et al, JPC 1995) said that this parameter set (called glycam93 in the AMBER program) was developed in agreement with the old AMBER force field (Weiner et al, JACS 1984, called parm91), but it might also be used with the new developed AMBER parameters (Cornell et al, JACS 1995, called parm94) because of the similar philosophy of assignment of atomic charges (both parm94 and glycam93 use RESP charges from HF/6-31G*, whereas parm91 used HF/STO-3G). Regarding to the coupling of glycam93 and parm94 we have several questions: 1. Does anybody know if these parameter sets should be coupled in principle? 2. If one can do so, which scaling factor of 1-4 nonbonding interactions should be used (0.5 as for parm91 and as used in Woods' paper for parameterization, or 0.83 as for parm94)? 3. The Woods paper refers to some parameters in the GLYCAM force field which were adopted from the parm91 parameter set. Should these parameters be used from parm91 also for the coupling with the parm94 set or should they be replaced by the new parm94 parameters, which are a bit different? Thank you for your assistance. Bernd Kallies -- Dr. Bernd Kallies University Potsdam Institute for Physical and Theoretical Chemistry Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm Tel : [+49] (0)331 / 977-1313 Fax : [+49] (0)331 / 977-1315