From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Wed Oct 19 2022 - 16:23:37 CDT

I want to bond two separate proteins together. In VMD I have used topo addbond and it creates one, but then when I save it and try to make a PSF, the bond is gone and autopsf has added hydrogens to the atoms on the residues I want to join in a peptide bond. I've tried adding a bond in PyMOL and the bond gets added, but then it's not there in VMD when I try to setup my simulation. What is the best/easiest way to join two proteins together? Thanks!

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017