From chemistry-request@server.ccl.net Mon Sep 13 08:56:59 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA13856 for ; Mon, 13 Sep 1999 08:56:59 -0400 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA01352 for ; Mon, 13 Sep 1999 08:51:33 -0400 (EDT) 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 IAA09882 for ; Mon, 13 Sep 1999 08:51:19 -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 KAA27139 for ; Sat, 11 Sep 1999 10:34:48 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id KAA43856 for chemistry@www.ccl.net; Sat, 11 Sep 1999 10:34:48 -0400 (EDT) Message-Id: <199909111434.KAA43856@pellan.CERCA.UMontreal.CA> Subject: 1) Ab Initio 2) HIV Protease To: chemistry@www.ccl.net Date: Sat, 11 Sep 1999 10:34:47 -0400 (EDT) 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 lot of experience with DFT and little with HF/Post-HF. 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 to optimizing minima and TS followed with an 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. Is this the best possible approach? 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. My question is: is there a water molecule in the active site of the wild type enzyme or there is no water molecule. Kind Regards to all of you. Suzanne Sirois