VMD-L Mailing List

From: Aditi Gotkhindikar (aditi.got_at_gmail.com)
Date: Sun Jan 23 2022 - 23:55:55 CST

Hello,
I have a dcd file of a protein-ligand simulation . I am facing the problem
of pbc wrap. The ligand is moving in and out of protein in the overall time
period.
I tried the command below but couldn't solve the problem.
command -
1. pbc wrap -centersel "protein" -center com -compound residue -all

Please can you suggest a solution to the problem.

Thank you
Aditi