[AMBER] Volume occupied during MD

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Thu, 15 Mar 2018 13:31:28 +0000


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. Iíve 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? Havenít 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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Received on Thu Mar 15 2018 - 07:00:02 PDT
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