VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Aug 18 2020 - 00:32:47 CDT

For 1, 'free' is for a single amino acid.
For 2, from a technical standpoint you ought to be able to modify the
fix_martini_psf.tcl script to set the disordered regions to 'C'. But it is
probably important to think carefully about whether this is a good idea at
all; IDPs are tricky business even for good all-atom force fields, so you
ought to be very sure that the questions that you're interested in could be
answered in a meaningful way with a CG approach, especially if you're
looking at protein-protein interactions.
Best,
Peter

On Wed, Aug 12, 2020 at 3:27 PM Ritu Arora <ritu.arora_at_mail.concordia.ca>
wrote:

> 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
>