From: Gumbart, JC (gumbart_at_physics.gatech.edu)
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.
Best,
JC
On Mar 7, 2021, at 6:15 PM, Ropon-Palacios G. <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>> 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
writepdb
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