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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 05 2011 - 02:30:02 PST
