VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Thu Oct 31 2013 - 12:48:46 CDT

well, if you own Accelrys Materials Studio, or Cerius 2, you may use the
volume calculation tool. It allows you to compute exact van der Waals
volume and surface of the molecules, and if periodic boundaries are used it
will also calculate fractions of occupied space and free volume.

the free volume is the space between the atoms, where a probe can be
inserted without an overlap with any of atoms. the probe in the program can
be set to have a zero point radius - then the free volume quantity obtained
is called empty space. if non zero radii are considered, you obtain a probe
accessible, or occupiable volume. usually a probe radius obtained as a
weighted average of atomic radii which constitute the molecule is
consedired, often giving R = ~1.4 A. with the probe of this radius you
obtain free volume cavity with smoothed surface and interstitial volumes
are neglected - this is perhaps how atoms see each other.

if you need to consider also atomic movements, as Axel mentionned, usually
you may consider the amplitude of mean square displacement (MSD) obtained
for example from neutron scattering. but note, that when increasing the
atomic radii the free volume will drop very fast. in one of our works we
also attempted a more rigorous approach, when we overlapped atomic
structures from trajectory, so that amplitude of atomic vibrations took
into account also a local situation of atoms and particular amplitude of
each atom, not only the averaged one as from MSD.

but i think that what you are looking for is just calculation of the volume
of channel, and you may use van der Waals radii of atoms, and a probe with
zero radius. if you increase the radius of the probe, the free volume
calculated scales with the probe radius so it is sufficient to calculate
free volume for only one probe radius. for this you may use any software
that calculates the free volume in a periodic box. you may prepare a
script, that puts additional atoms everywhere around the channel and run
the calculation. if you don't have Accelrys software you should look for
Connolly's routine, i have found some open codes some time ago. a FORTRAN
 code for Connoly is available also within Tinker molecular modeling
package. or you should look for some probing codes by Rigby and Roe etc.

dudo

On Thu, Oct 31, 2013 at 5:00 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
> 

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