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 Tue Sep 07 2010 - 07:30:07 PDT
