I have used desmond of schrodinger to conduct 100 ns simulation for my protein-ligand complex, now want to perform DCCM analysis, to perform it using Bio3D package of R, DCD file is needed. Desmond generates out.cms and .dtr files. how can I convert these into DCD file for DCCM analysis.

I have used VMD for the conversion but in Rstudio it gave error saying "check header data is correct, particulary the number of atoms"

How to solve, please help.

Error messages:

> traj fit plot.dccm(dccm_matrix) Error: object 'dccm_matrix' not found

My R script that I have used:

library(bio3d)

pdb