From: Ashar Malik (
Date: Fri Mar 24 2023 - 19:38:09 CDT

If the atoms dropped are terminal atoms they are applied as patches.

Autopsf provides this section where you can apply N and C terminal patches
of your choice. Apply the ones that the starting system has to conserve the
number of atoms.

Patch atoms are “patch” atoms to add properties to ends of the protein.
They ‘modify’ the terminal amino acid. They do not change protein length or
amino acid sequence unless your sequence analysis program has the
capability to detect a modified amino acid as different from its native

Hope this helps.

On Sat, 25 Mar 2023 at 4:34 AM, Priyanshu Gupta <>

> Hello,
> 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.
> Sincerely,
> Priyanshu R Gupta