On Wed, Mar 31, 2010, maya maya wrote:
>
> i am tring to do Generalized Born Approach for DNA ,
> In the tutorial file i saw the normal minimization procedure
> and i gave the igb=2 ,
The only variant of GB that has been extensively tested for DNA is igb=1,
and I would recommend using that. This is the value used in Amber's
"basic tutorial 1". I'm not sure what tutorial file you are are using.
> for equillibration i saw in earlier tutorial (
> http://www2.umdnj.edu/~kerrigje ) script as follows
I don't see exactly what you must be looking at, but I'd suggest you try
tutorial B1 at htpp://ambermd.org/tutorials if you have not already done so.
....dac
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Received on Wed Mar 31 2010 - 12:00:03 PDT
