VMD-L Mailing List

From: Neeraj Dhandia (nirajd_at_iitk.ac.in)
Date: Fri Oct 14 2022 - 06:45:08 CDT

Hello VMD users,

I have come across 2 problems:

- I am currently trying to make psf file of a protein chain (PDB ID:
1USZ), but after running automatic psf builder, it breaks into two chains.
I am currently using CHARMM V.47 topology files. How could i avoid this?

- Same cystine residue is written twice in the output pdb file with
different atom positions after running automatic psf builder. I am using
protein, PDB ID: 3VOR. Should i be worried about this or ignore this??

Any suggestion to understand this behavior would be very helpful.

Thank you and Best Regards,
Neeraj Dhandia
BPCL LAB
IIT KANPUR, INDIA