VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Mon Nov 04 2013 - 11:02:04 CST

https://www.researchgate.net/publication/237086256_The_Free_Volume_Dynamics?ev=prf_pub

On Thu, Oct 31, 2013 at 6:48 PM, Dudo <dudomail_at_gmail.com> wrote:

> 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.
>>
>
>
>
> --
> ____________________
> Ing. Dusan Racko, PhD
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 3229 4321
> 

-- 
____________________
Ing. Dusan Racko, PhD
Polymer Institute of the Slovak Academy of Sciences
Dubravska cesta 3
845 41 Bratislava, Slovak Republic
tel: +421 2 3229 4321