Re: Patch bond not formed

From: Kodituwakku,Dimuthu Nirmani (
Date: Sun Jun 28 2020 - 16:46:19 CDT

Hi Josh,

Thanks for the reply. I found that bond exists ( by checking the atom numbers) in my psf file. But it doesn't show in vmd when I load the both psf and pdb file.

Any reason for that? And I checked several times the order looks fine when compared to the topology file for the patch.


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From: Josh Vermaas <>
Sent: Sunday, June 28, 2020 5:42:45 PM
To: NAMD list <>; Kodituwakku,Dimuthu Nirmani <>
Subject: Re: namd-l: Patch bond not formed

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Looks perfectly reasonable at first glance. Anything in the log that sticks out to you? I'd also double check that you have the residue order listed in the patch is correct, since having them listed backwards will just silently do the wrong thing and not tell you.


On Sun, Jun 28, 2020 at 12:01 AM Kodituwakku,Dimuthu Nirmani <<>> wrote:

I'm trying to form a bond between asparagine residue of the protein and NAG. I renamed BGLCNA as BGL in the toppar_all36_carb_glycopeptide.str file. I see that the corresponding H and O atoms getting deleted but the bond is not formed. I have copied my .pgn file below.


package require psfgen
topology top_all36_prot.rtf
topology top_all36_carb.rtf
topology toppar_all36_carb_glycopeptide.str
topology toppar_water_ions_namd.str
topology topfadA_h.rtf
topology top_all36_cgenff.rtf
segment U {
pdb fad.pdb }
coordpdb fad.pdb U
pdbalias residue NAG BGL
pdbalias residue BMA BMAN
pdbalias residue MAN AMAN
pdbalias residue GLUP GLU
pdbalias residue ASPP ASP
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment 1gpA {pdb 1GPEHA.pdb
regenerate angles dihedrals
segment 1gpB {pdb 1GPEHB.pdb
regenerate angles dihedrals
segment nag { pdb nag.pdb
regenerate angles dihedrals
segment bma { pdb bma.pdb
regenerate angles dihedrals
segment man { pdb man.pdb
regenerate angles dihedrals
patch DISU 1gpA:168 1gpA:210
patch DISU 1gpB:168 1gpB:210
patch GLUP 1gpA:55 1gpA:60 1gpA:303 1gpA:416 1gpB:55 1gpB:60 1gpB:303 1gpB:416
patch ASPP 1gpA:431 1gpB:431
patch NGLB 1gpA:93 NAG:1
patch 14BB NAG:1 NAG:2
patch 14BB NAG:11 NAG:12
patch 14BB NAG:7 NAG:8
patch 14BB NAG:17 NAG:18
patch 14BB NAG:12 BMA:13
patch 13BA BMA:13 MAN:14
patch 12AA MAN:14 MAN:15
patch NGLB 1GPB:93 NAG:11
patch 14BB NAG:2 BMA:3
patch 14BA BMA:3 MAN:4
patch 12AA MAN:4 MAN:5
patch NGLB 1GPA:392 NAG:9
patch NGLB 1GPB:392 NAG:19
patch NGLB 1GPA:357 NAG:7
patch NGLB 1GPB:357 NAG:17
patch NGLB 1GPA:165 NAG:6
patch NGLB 1GPB:165 NAG:16

regenerate angles dihedrals
coordpdb nag.pdb nag
coordpdb bma.pdb bma
coordpdb man.pdb man
coordpdb 1GPEHA.pdb 1gpA
coordpdb 1GPEHB.pdb 1gpB
writepdb gpe.pdb
writepsf gpe.psf

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