Hi,
The detail of H-bond calculcation is given in mentioned tutorial (
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/section6.htm).
You can modify the parameter according to your file system.
Best,
Hirdesh
On Wed, Sep 8, 2010 at 3:46 PM, <monica.imtech.res.in> wrote:
> hi
> i'm actually new to amber
> i just want to know how to calculate h-bonds from the trajectory files
> using ptraj.
> ur help will be highly appreciated.
>
> thanx
> monica
>
>
>
>
>
>
> > Hi AMBER Users,
> > I am interested in calculating the duration for a particular H-bond for
> > trajectory files. What I am able to calculate is the percentage for a
> > particular hydrogen bond. Suppose the H-bond is made in between two
> residues
> > (A and B say) during the simulation. What I get from ptraj analysis is
> the
> > percentage of H-bond (say 50% in between A and B). But I am more
> interested
> > in calculating the trajectories in which the H-bond is formed and the
> > trajectories in which the bond is not present between two residues.
> > Hope my doubt is understandable. I am interested in calculating whether
> out
> > of 50% H-bond between A and B residues, the H-bond is formed like
> 10%(1-10
> > trajectories say) then 30%(40-70 trajectories) and then last 10%( during
> > 90-100 trajectories).
> > Any help regarding this will be appreciated.
> > Thanks,
> > Hirdesh
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> >
> >
>
>
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--
Thanks and Regards,
Hirdesh,
******************************************
Hirdesh Kumar
PhD Scholar
School of Biological Sciences
Indian Institute of Technology, Delhi
Hauz Khaas, New Delhi-16
http://www.iitd.ac.in/bioschool.html
******************************************
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Received on Wed Sep 08 2010 - 04:00:03 PDT
