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

[banafsheh mehrazma]

Dear Mark;
Thank you for your instant reply. You are right, but in my case, there is a residue  8-OxoG  (oxidized G). As you know, in all of the force fields in Gromacs package, G,C,A and T are known. In your opinion, what should I do in case of 8-OxoG, to obtain parameters needed for this new residue?
    Thank you
   B.Mehrazma


________________________________
 From: banafsheh mehrazma <bmehrazma at yahoo.com>
To: gmx-users at gromacs.org 
Sent: Saturday, December 24, 2011 3:11 PM
Subject: [gmx-users] Fw: modifying the mutated DNA parameters
 



--- 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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