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
Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at
http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via
https://csirt.uct.ac.za/page/report-an-incident.php.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 15 2018 - 07:00:02 PDT
