Thanks Aneesh but I am already using Amber Tools 1.4 with Amber11 and not
getting such form of result.
> On Tue, Jan 4, 2011 at 1:09 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Thank you Aneesh for reply.
>>
>> Here I want to know one more thing what is the default value of time, Is it
>> 1 ?
>>
> yes. It is.
>
>>
>> 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 ?
>>
> You can download and use Amber 1.4 tools
>
> regards,
> Aneesh
>
>>
>>
>>
>> > 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
>> >>
>> >>
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>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
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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 Wed Jan 05 2011 - 04:00:02 PST
