AMBER Archive (2009)

Subject: Re: [AMBER] basepair

• Previous message: Vikas Sharma: "[AMBER] chosing complex in amber"
• In reply to: balaji nagarajan: "[AMBER] basepair"
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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_at_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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• Previous message: Vikas Sharma: "[AMBER] chosing complex in amber"
• In reply to: balaji nagarajan: "[AMBER] basepair"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]