VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Mar 08 2017 - 09:54:21 CST

Hi Daniela,

Could you paste in the rest of your script? The patch command looks right (assuming the segnames/resids are correct), so assuming you write out your pdb/psf pair afterward and load them in, the bond should totally exist.

-Josh

On 03/07/2017 08:33 PM, Daniela Rivas wrote:
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.