From: John Stone (
Date: Thu Oct 31 2013 - 10:05:24 CDT

  There's no built-in tool that would do precisely what you have in mind.
You may need to investigate why the online tools you mentioned behave the
way they do, there's undoubtably a logical reason that they have the
limitation you describe.

  John Stone

On Wed, Oct 30, 2013 at 02:14:54PM +0530, Revthi Sanker wrote:
> Dear all,
> I am working on a channel protein, which is inhibited due to the physical
> blocking of the channel by an inhibitor. I would like to calculate the
> %volume of the channel occupied by the inhibitor i.e volume fraction of
> the inhibitor. I found several online servers for volume calculation but
> all of them do not provide the volume of the whole channel instead divide
> it into discontinuous sub-pockets . Is there any analysis tool/plugin in
> VMD that will help me in this analysis?
> Kindly provide your valuable suggestions.
> Thank you in advance.
> Revathi.S
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
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