Re: area of a hydrophobic patch

From: Aaron Oakley (
Date: Thu Feb 03 2005 - 16:35:56 CST

Do you mean the surface area or volume?

You could use the "sasa" command in the latest
VMD release (1.8.3a?). It performs reasonably

On 03/02/2005, at 4:23 PM, Narender Singh Maan wrote:

> 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
> singh
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