Hi,
If you use the latest GitHub version of cpptraj
(
https://github.com/Amber-MD/cpptraj) the total volume occupied by
voxels from the volmap command each frame is saved as <set
name>[totalvol]. Note that unless you're doing some kind of fitting to
remove global translations/rotations, they will be included in the
volume estimates.
Hope this helps,
-Dan
On Thu, Mar 15, 2018 at 9:31 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> Hi
>
> I have simulated the behaviour of 2 glycoproteins (homologs) and would like to compare the volume occupied at each glycan site between the two proteins. This would identify changes in their dynamic range due to unique protein interactions etc. I’ve used VMD to produce and visualize .dx occupancy volmaps and observed differences.
> Is there any way in which I can calculate exact volume values per glycan in cubic angstroms to quantitatively compare? Haven’t found a way to do this in vmd and saw that amber has a volmap function as well.
> I want an output like fig 2 in Yang et al 2017 (doi:10.1038/s41598-017-04532-9)
>
> Kind regards
>
> Lizelle Lubbe
> PhD Chemical Biology
> University of Cape Town
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 10 2018 - 06:30:04 PDT
