VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Oct 20 2022 - 04:12:11 CDT

Hi Kelly,

what kind of bond would that be? Is there a topology and FF parameters for the chemical surroundings of such a bond?

Jerome

----- Le 19 Oct 22, à 23:23, Mcguire, Kelly <klmcguire_at_UCSD.EDU> a écrit :

> 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