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

[banafsheh mehrazma]

Dear all; 
 As you all  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?  How to obtain parameters needed for this new residue?
  Thank you 
 B.Mehrazma

________________________________
 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, December 25, 2011 10:58 AM
Subject: Re: [gmx-users] Fw: modifying the mutated DNA parameters
 

On 12/25/2011 6:04 PM, banafsheh mehrazma wrote: 
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?
>
You're assuming that you need a new atom type and/or bonded
    parameters for your force field. You have to determine whether that
    is true, yet.

Mark

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