VMD-L Mailing List

From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Tue Mar 07 2017 - 20:40:19 CST

Hi all,

I have generated the PSF file for my system, patching the N-glycosylation
as follows:

patch NGLB P1:180 O1:331

Where P1 is my protein and O1 is the sugar.

My script for building the PSF runs perfectly with no errors, but when I
open the new PSF and PDB files I cannot see the bond between the protein
and the sugar. I noticed that the correct Hydrogen and Oxygen atoms have
been deleted, but somehow the bond is not there.

Has anyone else have an issue like this before? Am I missing something?

Cheers,
Daniela.