Re: Patch bond not formed

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sun Jun 28 2020 - 16:42:45 CDT

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.

-Josh

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

> Hello,
>
> 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.
>
> Thanks.
>
> 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
> guesscoord
> writepdb gpe.pdb
> writepsf gpe.psf
>
>

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