VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Aug 29 2020 - 23:21:49 CDT

How did you try visualizing your file? The bond is present in the psf --
see here in the BONDS section:

51826 51828 51826 51827 51826 51819 51829 4839

So the last entry in that row is a bond between the ND2 atom of N331 to the
C1 atom of your BGLN4 residue.
Best,
Peter

On Sat, Aug 29, 2020 at 6:18 AM Adupa Vasista <adupavasista_at_gmail.com>
wrote:

>
> Dear VMD Users,
> I am generating PSF using AutoPSF plugin in VMD version 1.9.4a38, My
> molecule contains a protein and a sugar. AutoPSF recognizes the required
> patches, So I generated the PSF and the process went smoothly. But when I
> visualize it by loading into VMD, I do not see any bond between the sugar
> and protein. Am I missing anything?
>
> The only change I made in the topology file(top_all36_carb.rtf) is
> changing the residue names from BGLCNA and BGLCN0 to BGLN.
>
> I also tried to apply the patch manually taking the patching information
> from AutoPSF, but results in an error saying
> *patch NGLB AP1:331 DG1:4*
>
> *psfgen) applying patch NGLB to 2 residue(s)*
> *psfgen) no segment AP1*
>
> I have checked for that segname, It is present, but still the error
> exists.
>
> Help me in this regard.
>
> Here, I attach the pdb of the molecule and the psf generated by AutoPSF.
>
> I am Sorry, if the mail came twice.
>
> Thank you.
>
>
>
> 6vxx_model_01_chainD_autopsf.psf
> <https://drive.google.com/file/d/1kNodhx6aPj3wKZErGXSN-TY-koRx6xHr/view?usp=drive_web>
>
>
> 6vxx_model_01_chainD.pdb
> <https://drive.google.com/file/d/11Y6ZPsulCqT6T3zlViAle9niRlBAskNM/view?usp=drive_web>
>
>