From chemistry-request@server.ccl.net Sun May 20 11:07:30 2001 Received: from sgi04-e.std.com ([199.172.62.134]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4KF7TI21785 for ; Sun, 20 May 2001 11:07:29 -0400 Received: from world.std.com (world-f.std.com [199.172.62.5]) by sgi04-e.std.com (8.9.3/8.9.3) with ESMTP id LAA14636237 for ; Sun, 20 May 2001 11:07:29 -0400 (EDT) Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id LAA23091 for chemistry@ccl.net; Sun, 20 May 2001 11:01:54 -0400 (EDT) Date: Sun, 20 May 2001 11:01:54 -0400 (EDT) From: Joe M Leonard Message-Id: <200105201501.LAA23091@world.std.com> To: chemistry@ccl.net Subject: Two areas of interest Folks, I am interested in learning whether anybody has looked into the following areas recently: (a) Investigating the effect of conformation on surface area and volume. This would also include models predicting such. (b) Conformational analysis. If anybody has collected "the literature base", particularly for the last 2+/- years, I would appreciate hearing from them! All information welcome - I will summarize what I get for the net. Thanks in advance! Joe Leonard jle@world.std.com From chemistry-request@server.ccl.net Sun May 20 17:07:47 2001 Received: from mb2i0.ns.pitt.edu ([136.142.186.36]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4KL7lI27668 for ; Sun, 20 May 2001 17:07:47 -0400 Received: from imap.pitt.edu ("port 1221"@[136.142.122.87]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01K3SLXPOD9C012195@mb2i0.ns.pitt.edu> for chemistry@ccl.net; Sun, 20 May 2001 17:07:45 EDT Date: Sun, 20 May 2001 17:09:27 -0400 From: Artem Mamonov Subject: ALA carbonyl flip in alpha helix protein To: chemistry@ccl.net Message-id: <3B083287.8030403@imap.pitt.edu> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; m18) Gecko/20001108 Netscape6/6.0 X-Accept-Language: en Dear all, Working on MD simulations (AMBER6, parm96.dat) of a small alpha helix protein (gramicidin A) i've noticed that some ALA carbonyls of the backbone flip over (~180 degrees) along the helix. I am wondering if it can take place in a real life or it's a drawback of the force field/parametrisation/methodology. I will appreciate any comments/references. thanks -- Artem Mamonov Graduate Student Department Of Chemistry University Of Pittsburgh email: artem@imap.pitt.edu