VMD-L Mailing List

From: Sandra Rennebaum (Sandra.Rennebaum_at_rwth-aachen.de)
Date: Mon Aug 23 2010 - 03:44:34 CDT

Dear all,

I am a beginner to VMD and tried to use the 'pbc unwrap' command because I have big jumps in the coordinates of the atoms of my MD simulation of a protein and a ligand.
However, after the unwrap command the structures of both protein and ligand are distorted (e.g. they show unreasonable bond angles).

The vmd script I use is this:

------------------
mol load pdb complex.pdb dcd complex.dcd

set sel [atomselect top all]

pbc wrap -centersel protein

pbc unwrap -sel all

animate write dcd dyn_unwrap.dcd beg 1

mol delete all

quit
----------------

I get no error messages whatsoever. I also tried to remove the wrap command and tried to add 'pbc join bonded', but nothing helped.
Before the unwrap command the structure looks absolutely fine.
I appreciate any help.

Thank you very much,

Sandra