Dear amber users,
I have performed Random Acceleration Molecular Dynamics(RAMD)simulations
using amber8 in order to explore exit trajectories of a ligand from its
docking position in the buried active site of the enzyme. Now, I would like
to analyze the obtained RAMD trajectories. For this purpose, I want to
identify the residues lining each substrate-exit channel found from RAMD
simulations. For this, the closest distance between any protein atom and any
ligand have to be determine at each x time step. Moreover, I would to
determine the frequency of residues recording to known the amino acid which
are the most frequently in close contact with the substrate along the
trajectories.
Do you known a method to get these data from my trajectories? Do you think
these informations can easly be obtained with ptraj ? Do you have some
scripts to do this ?
Thank you very much for your help !!!
Sincerely,
Sophie
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Received on Tue Jul 20 2010 - 06:00:04 PDT
