Could someone please explain to me how the non-bonded interaction
parameters are determined? Are the usual mixing rules applied? Here's a
piece of param99.dat from the website:
MOD4 RE
OH 1.7210 0.2104 OPLS
CA 1.9080 0.0860 Spellmeyer
So what are the parameters for an OH-CA interaction? Are the following
true:
sigma = (1.721 + 1.9080)/2
epsilon = (0.2104*0.086)^0.5
non-bonded-energy = epsilon/4*[(r/sigma}^12 - (r/sigma)^6]
Kevin Van Workum
www.tsunamictechnologies.com
From rajaamber6_at_rediffmail.com 28 Aug 2001 17:28:04 -0000
Message-id: <20010828172804.13589.qmail.mailweb19.rediffmail.com>
Date: 28 Aug 2001 17:28:04 -0000
From: Raja Swaminathan <rajaamber6_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: group input
In-Reply-to: <20010827084651.17585.qmail.web12501.mail.yahoo.com>
Sir
I am using AMBER for my minimization procedures. In that i want to use group input option for my protein structure. (i.e) i want to minimize my protein by constraining backbone only and allowing all the other side chain torsions free.
Please advice me in this regard and provide a sample input of the same.
Thanking you in advance
Raja
Received on Mon Aug 27 2001 - 09:10:24 PDT
