From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sun Jun 28 2020 - 17:33:31 CDT
Which file do you load first? If you load the pdb first, VMD will guess
bond topologies from interatomic distances. When you then load the psf, no
new information is added. Load the psf first, and then the bond should be
visible.
-Josh
On Sun, Jun 28, 2020 at 3:47 PM Kodituwakku,Dimuthu Nirmani <
dkodituwakku_at_ufl.edu> wrote:
> 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.
>
> Thanks.
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------------------------------
> *From:* Josh Vermaas <joshua.vermaas_at_gmail.com>
> *Sent:* Sunday, June 28, 2020 5:42:45 PM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>; Kodituwakku,Dimuthu Nirmani <
> dkodituwakku_at_ufl.edu>
> *Subject:* Re: namd-l: Patch bond not formed
>
> *[External Email]*
> 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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