Balaji,
If i understand correctly, you want to track the hydrogen bonding between
the bases. You can try hbond in ptraj to see the life time of hydrogen bonds
and % occupancy or alternatively you can monitor the heavy atom distances.
Search amber mail archieve for hbond analysis.
Bala
On Fri, Apr 10, 2009 at 7:30 AM, balaji nagarajan
<balaji_sethu.hotmail.com>wrote:
>
> Dear amber ,
>
> I have done dynamics of DNA ,
> I would like to check the existance of basepair in DNA trajectory with
> respect to time ,
> is it possible to do with ptraj ?
>
> or else how to do it .
>
>
> thanks in advance
> balaji
> UOM
>
>
>
>
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Received on Wed Apr 15 2009 - 01:14:19 PDT
