From chemistry-request@server.ccl.net Mon Sep 13 09:46:31 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA14063 for ; Mon, 13 Sep 1999 09:46:31 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id JAA25637 for ; Mon, 13 Sep 1999 09:41:07 -0400 (EDT) Received: from pellan.CERCA.UMontreal.CA (pellan.CERCA.UMontreal.CA [132.204.150.49]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id JAA10548; Mon, 13 Sep 1999 09:41:15 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id JAA46574; Mon, 13 Sep 1999 09:41:14 -0400 (EDT) Message-Id: <199909131341.JAA46574@pellan.CERCA.UMontreal.CA> Subject: 1)Ab initio 2) HIV-PR To: chemistry@ccl.net Date: Mon, 13 Sep 1999 09:41:14 -0400 (EDT) Cc: siroiss@CERCA.UMontreal.CA (Suzanne Sirois) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers First Question; ab initio calculations I have been using DFT for various types of H-bonded systems and to my knowledge it is fast and reliable. I would like to perform some ab initio calculations. I have a system of about 20 atoms containing very important H-bonds. What will be the State-of the Art for optimizing the minima and TS and then examining the IRC. Someone suggested to me to do the following: Perform a full optimization at RHF/6-31G** of the 2minima and TS. Connect the TS to the two minima with IRC using the GS2 method at the RHF/6-31G**. Then perform an MP2 single point calculation on the 2 minima and TS for obtaining a better energy. Second Question: I am a little confuse with the following: In JACS 118, 3946 (1996) Citing the author: " It follows from this structure (ref. Wlodawer et al. Science 1989, 245, 616-621) that the two side chains of Asp25-and Asp-25' of the active site are planar with a structural water bound to both." I have downloaded the PDB file: 3HVP and there is no water molecules attach to it. Is there a water molecule in the active site of the wild type enzyme or there is no water molecule. In fig.4 Science 245, 616 (1989). The authors mention: "Active site electron density showing a density for a water molecule which is found in similar position in all native structures of aspartic proteases." (Could it be a density for something else (NH4+?). "The distance of this water from the carboxylate O atoms is slightky greater than expected". (Why modeling the HIV-Pr with a water molecule in the catalytic site cleft if the crystal structure reveals that the water is at a distance greater than expected?) Kind Regards to all of you. Suzanne Sirois