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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Received on Wed Sep 08 2010 - 03:30:03 PDT
