VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Oct 31 2013 - 11:00:24 CDT

On Thu, Oct 31, 2013 at 4:05 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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.

i would say the reason is that this is an ill defined quantity in the
first place, especially with everything moving around and considering
that things on the atomic scale are not quite the way we imagine them
to be in our macroscopic world.

axel.

>
> 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/ 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.