[gmx-users] Fw: modifying the mutated DNA parameters

[banafsheh mehrazma]

--- On Sat, 12/24/11, banafsheh mehrazma <bmehrazma at yahoo.com> wrote:


From: banafsheh mehrazma <bmehrazma at yahoo.com>
Subject: 
To: gmx-users at gromacs.org
Date: Saturday, December 24, 2011, 3:39 AM







To whom it may concern;
I am willing to study a damaged DNA which has a 8-oxoG as the lesion (the Carbon 8 in guannine is oxidized.). I have the following questions;
1) Should I change the sigma and epsilon parameters in the force field that I want to work on? and how?
2) Should I change the bonded parameters in the force field? and how?
3) The new charges for the lesion are obtained from Gaussian package; where can I  mention the modified charges?
 
Thank you for your regards
B.Mehrazma
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