VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Sat Aug 29 2020 - 03:21:23 CDT

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>