VMD-L Mailing List

From: Ritu Arora (ritu.arora_at_mail.concordia.ca)
Date: Wed Aug 12 2020 - 12:34:41 CDT

Hi,

I am trying to do residue-based coarse-graining on a system comprising of a protein-protein complex. One of the proteins consists of an intrinsically disordered region of 25 residues (not present at the terminal of the protein). I am following the RBCG tutorial and right now, I am at step: MARTINI mapping/correction for protein secondary structure. I have two questions in regards to coarse-graining:

  1.
The RBCG tutorial mentions -

"Backbone beads may be classified as Helix (H), Coil (C),Extended (E), Turn (T), Bend (B) or Free (F)."

How is a 'Free' bead defined here and how is it different from the 'Coil' conformation? Also, fix_martini_psf.tcl doesnot mention the 'Free' label in the lists of label conventions used by STRIDE and DSSP. Is the Free label accounted in 'none of the above or error' category?

  2.
 When I use fix_martini_psf.tcl script for my system, the script labels the residues of disordered region as T, E, B, etc and not as C/F for all the residues. Hoping that I have to manually change the labels to 'C' or may be 'F'. I am not sure. Can you please suggest how to proceed?

Thanks and regards,
Ritu