From owner-chemistry@ccl.net Thu Nov 17 12:53:01 2011
From: "Yawen Li yl6c2|a|mail.missouri.edu" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: a question about making a parm file containing damino acids with LEaP
Message-Id: <-45893-111117125007-30282-lbfEz6gawauIZ6g78jPxAA*|*server.ccl.net>
X-Original-From: "Yawen  Li" <yl6c2[a]mail.missouri.edu>
Date: Thu, 17 Nov 2011 12:50:04 -0500


Sent to CCL by: "Yawen  Li" [yl6c2-#-mail.missouri.edu]
Hi, 

I am a beginner of the AMBER program. In the molecule I want to study, there is several D amino acids. But it seems to me that "source leaprc.ff99SB" do not have any D amino acids. How can I fix this problem and generate AMBER topology and coordinate files correctly?

By the way, I have to run the AMBER program on a university server, which means I have limited authority to modify the program. If it's possible, can anyone tell me how to fix this under my working directory.

Thanks a lot,
Yawen Li

Email: yl6c2~~mail.missouri.edu