From: Priyanshu Gupta (
Date: Fri Mar 24 2023 - 12:52:46 CDT

I have been working with the protein+membrane system provided with the
"Methods for calculating PMF" tutorial for NAMD. When I run AutoPSF on the
PDB file that comes with that tutorial, the system loses 6 atoms. On
checking the new PDB file generated with the original case, I see that
there are a few atoms being dropped at each terminal of the protein.
I expected this change to affect the sequence of the protein. However,
performing sequence analysis for the new and the old PDB files gave the
exact same sequence for both cases.

I am not sure why this may be happening or if I am doing something wrong.
Any insights would be appreciated.

Priyanshu R Gupta