From chemistry-request@server.ccl.net Sun Feb 9 16:53:32 2003 Received: from dh094-148.csb.sunysb.edu ([129.49.94.148]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h19LrWI16853 for ; Sun, 9 Feb 2003 16:53:32 -0500 Received: from dh094-148.csb.sunysb.edu (localhost.localdomain [127.0.0.1]) by dh094-148.csb.sunysb.edu (8.12.5/8.12.5) with ESMTP id h19LkZia016155 for ; Sun, 9 Feb 2003 16:46:35 -0500 Received: from localhost (cuigl@localhost) by dh094-148.csb.sunysb.edu (8.12.5/8.12.5/Submit) with ESMTP id h19LkYqQ016151 for ; Sun, 9 Feb 2003 16:46:35 -0500 X-Authentication-Warning: dh094-148.csb.sunysb.edu: cuigl owned process doing -bs Date: Sun, 9 Feb 2003 16:46:34 -0500 (EST) From: "CUI, Guanglei" X-X-Sender: cuigl@dh094-148.csb.sunysb.edu To: chemistry@ccl.net Subject: MEAD pKa calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers, I'm trying to use MEAD to calculate pKa of three residues in a ligand binding site. The structure has been minimized with AMBER force field with explicit solvent. The charges of these residues have been derived from RESP calculations. All needed files are created and multiflex calculation used epsin = 4.0. After the calculation, the intrinsic pKas of two residues are very surprising. So here's my questions: 1. What could be reasons that the self interactions for residue UNK and LYS are very big. 2. During the multiflex calculation, I was warned of "vertex found with count = 2" three times. How should I deal with this? 3. Do I need to include explicit solvent molecules in the calculation, generally speaking? The binding site is not completely buried. 4. LYS (protonated) has 3 equivalent hydrogens. It's not very clear to me which one should be zero charged in LYS.st file. Here're the .summ file. Sorry for the lengthy description. Any suggestions are welcome. Thanks in advance. site name pKmod delta self delta back pkint UNK-259 7.8 23.1134 -5.41211 25.5013 LYS-162 10.4 -11.4993 1.32968 0.23042 TYR-155 9.6 0.694971 -1.28149 9.01348 -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Sat Feb 8 05:24:25 2003 Received: from vimg1.rdg.ac.uk ([134.225.112.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h18AOPI24286 for ; Sat, 8 Feb 2003 05:24:25 -0500 Received: from vimv1.rdg.ac.uk ([134.225.16.87]) by vimg1.rdg.ac.uk (Exim: gateway) with esmtp id 18hS9o-0001Zl-00 for CHEMISTRY@www.ccl.net; Sat, 08 Feb 2003 10:24:24 +0000 Received: from vimh1.rdg.ac.uk ([134.225.16.83]) by vimv1.rdg.ac.uk (Exim: virusscanner) with esmtp id 18hS9i-0005oQ-00 for CHEMISTRY@www.ccl.net; Sat, 08 Feb 2003 10:24:18 +0000 Received: from suts1-p7.rdg.ac.uk ([134.225.114.7] helo=reading.ac.uk) by vimh1.rdg.ac.uk (Exim: host) with esmtp id 18hS9e-0003p2-00 for CHEMISTRY@www.ccl.net; Sat, 08 Feb 2003 10:24:14 +0000 Message-ID: <3E44DBAA.E85866E1@reading.ac.uk> Date: Sat, 08 Feb 2003 10:27:54 +0000 From: David Price X-Mailer: Mozilla 4.79 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: how to 'protect' point charges in Gaussian? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanner: exiscan *18hS9i-0005oQ-00*wvR6dt0JOzY* (The University of Reading) Fellow CCLers, I am trying to set up a calculation that has an oxide cluster surrounded by point charges, but want to restrict the ability of the oxide ions to polarise to much towards the positive point charges. The point charges are included to mimic other ions in a lattice and thus even the positive charges will repel the electron gas cloud of the oxide ions at some distance from the point charge corresponding to the positive ion's 'radius'. How do I do this in Gaussian? I thought of using pseudo-potentials centred on the positive point charges, but wasn't sure if I could get one the right shape. Help much appreciated. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9318453 (messages) Visiting Research Fellow, Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------