Thank you Aneesh for reply.
Here I want to know one more thing what is the default value of time, Is it 1 ?
In Amber tutorial:-
http://ambermd.org/tutorials/basic/tutorial3/section6.htm
Occupancy of H-bonding (last column)is define in form of time of MD run i.e.
percentage occupency is written after every 5ns of trajectory.
Is it possible in amber11 to get such form of result ?
> Dear Sangita,
>
> http://archive.ambermd.org/200503/0359.html
>
> Hope this link will help you.
>
> Regards,
> Aneesh
>
> On Mon, Jan 3, 2011 at 10:57 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I have to do H-bond analysis. I have aready ran ptraj for set of donor and
>> acceptor now I am not getting, how to
>> interprate the %occupency of H-bond during MD simulation.
>>
>> Can anybody please suggest me how to interprate the output file?
>>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Jan 04 2011 - 10:30:03 PST
