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.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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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