[AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER

From: Anindya Sarkar <axs849.case.edu>
Date: Thu, 13 Jan 2011 00:27:14 -0500

Hi Everybody,

I am running the MD simulations of a glycosylated protein using AMBER force
field ff99SB and GLYCAM_06. Can anybody tell me how to analyze the different
properties of the glycosidic residues of the glycosylation like RMSD, Radius
of gyration, dihedral angle calculation, cluster analysis, glycomaps etc
using AMBER or any other software package?
I have run my simulations with the NetCDF format of the trajectory and I
have already used ptraj for stripping the water and ions but anybody can
tell me how to extract the glycosylation only trajectory devoid of the
protein molecule and how can I put the glycans at the center of the
trajectory like the proteins with the command "image center familiar" in
ptraj. Whether this glycosylation only trajectory can be saved as dcd
extension file also.

Thanks in advance.
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Received on Wed Jan 12 2011 - 21:30:03 PST
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