On 12/24/2011 10:41 PM, banafsheh mehrazma wrote:
--- On *Sat, 12/24/11, banafsheh mehrazma /<bmehra...@yahoo.com>/* wrote:
From: banafsheh mehrazma <bmehra...@yahoo.com>
Subject:
To: gmx-users@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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