VMD-L Mailing List

From: Aditi Gotkhindikar (aditi.got_at_gmail.com)
Date: Tue Jan 25 2022 - 00:11:51 CST

---------- Forwarded message ---------
From: Aditi Gotkhindikar <aditi.got_at_gmail.com>
Date: Mon, Jan 24, 2022 at 12:04 PM
Subject: vmd-l: pbc wrap issue
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

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