area of a hydrophobic patch

From: Narender Singh Maan (
Date: Wed Feb 02 2005 - 23:23:24 CST

Dear NAMD users,
i am analyzing my NAMD simulation data of a small protein. In the
protein there's a
hydrophobic cavity/patch formed by 8 residues and which is very
dynamic. Now my studies involve
measuring the area of this cavity along the simulation (4000 frames).
Though there are some programs
available to do this but can only do so one frame at a time and can
cost me quite some time to analyze
and compile all 4000 frames. Any input/suggeastions on how to do it
all at once would be greatly appreciated.
thank you

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