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

[Mark Abraham]

On 12/24/2011 10:41 PM, banafsheh mehrazma wrote:
>
>
> --- 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?
>

You need to consider your molecule in the light of the existing atom and 
bonded interaction types for the force field you have chosen. Maybe you 
need new ones, maybe not. For 3, you should consider the advice here 
http://www.gromacs.org/Documentation/How-tos/Parameterization (so your 
Gaussian-based charges may not be useful at all), and 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. 
All of the above will need a thorough knowledge of chapter 5 of the manual.

Mark

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