Re: N-glycosylation bond not view after patching

From: Gumbart, JC (
Date: Sun Mar 07 2021 - 22:15:35 CST

Are you making two separate graphical representations, one for PROA and one for CARA? A bond will only be shown if both atoms are included in the same entry. I’ve made this oversight before.


On Mar 7, 2021, at 6:15 PM, Ropon-Palacios G. <<>> wrote:

Dear namd users,
I have generated the PSF file for my system, patching the N-glycosylation as follows:
patch NGLB PROA:343 CARA:1
Where PROA is my protein and CARA 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?
My script :

;# Script for generate topology
if {1} {
package require psfgen

;# Fix topology
topology ../../toppar_c36_jul20/top_all36_prot.rtf
topology ../../toppar_c36_jul20/top_all36_na.rtf
topology ../../toppar_c36_jul20/toppar_water_ions.str
topology ../../toppar_c36_jul20/top_all36_lipid.rtf ; ## lipids
topology ../../toppar_c36_jul20/top_all36_carb.rtf
topology ../../toppar_c36_jul20/stream/carb/toppar_all36_carb_glycopeptide.str

;# Protein select
mol new step1_pdbreader.pdb type pdb waitfor all
set sel [atomselect top "protein"]
set segnames [lsort -unique [$sel get segname]]
foreach segname $segnames {
    puts "Adding protein segname $segname to psfgen"
    #pdbalias residue HIS HSD
    #pdbalias residue CYSP CYS
    pdbalias atom ILE CD1 CD
    set seg ${segname}
    set sel [atomselect top "protein and segname $segname"]
    $sel set segid $seg
    $sel writepdb tmp.pdb
    segment $seg {pdb tmp.pdb}
    #regenerate dihedrals
    coordpdb tmp.pdb $seg
    guesscoord ;## adiciona, H, y algunos atomos perdidos.

if {1} {
;# Glycan select
set sel [atomselect top "hetero and not protein"]
set segnames [lsort -unique [$sel get segname]]
foreach segname $segnames {
    puts "Adding glycan segname $segname to psfgen"
    pdbalias residue ANE ANE5AC ; ## carbohydrates
    pdbalias residue BGL BGLCNA ; ## carbohydrates
    #pdbalias residue BGL NGLA
    pdbalias residue AMA AMAN
    pdbalias residue BMA BMAN
    pdbalias residue BGA BGAL
    pdbalias residue AFU AFUC
    pdbalias residue AGA AGALNA
    set seg ${segname}
    set sel [atomselect top "hetero and not protein and segname $segname"]
    $sel set segid $seg
    $sel writepdb tmp.pdb
    segment $seg {pdb tmp.pdb}
    coordpdb tmp.pdb $seg
    #regenerate angles
    guesscoord ;## adiciona, H, y algunos atomos perdidos.

if {0} {
##; Patching Disulfide bonds
patch DISU PROA:131 PROA:166
patch DISU PROA:291 PROA:301

##; Patching glycans
##; information was get from: step1_pdbreader_glycan.str charmm-gui
##; forward
patch NGLB PROA:343 CARA:1
patch NGLB PROB:90 CARB:1
patch NGLB PROB:103 CARC:1
patch NGLB PROB:53 CARD:1
patch NGLB PROB:322 CARE:1
patch NGLB PROB:546 CARF:1

;# Escribiendo los output
writepsf wildtype_top.psf ; # Output PSF

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