specifying bonds between 2 residues
Created by: vsbgithub
I am attempting to generate a CG model for a polymer using pycgtool. I have already set-up and run the atomistic system for the polymer in a solvated environment.
I was able to get the CG mapping scheme to work and generate a CG.gro file using your tool. However, I had to specify 3 residue types in the polymer (namely start, middle and end residues). Note that each residue consists of 3 types of beads.
I had to consider 3 residues since the number of atoms on the start, middle and end residues for any polymer will be different and hence I cannot get the mapping scheme to work if I only consider a single residue type.
Since the start residue is bonded to the middle residue which in turn is bonded to the end residue, I was wondering how it'd be possible to specify this in the .bnd file. The examples all consider CG systems that only consist of 1 residue type.
How do we specify bonds between beads belonging to different residue types in pycgtool?
Would this even be possible or is it only possible to have bonds within a residue?
Thank you. Vivek