VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 31 2013 - 10:05:24 CDT

Hi,
  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.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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
> ______________________________________________
> International Conference on Bimolecular Simulations and Dynamics
> Official website:
> http://cmsrv.iitm.ac.in/icbsd2013/
> _______________________________________________ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/