VMD-L Mailing List

From: Marawan Hussien (marawanhussain_at_REMOVE_yahoo.com)
Date: Wed Jun 24 2015 - 15:51:57 CDT

Hi,I am simulation an ion channel embedded within a POPC membrane built through CHARMGUI and simulated with NAMD . The ion channel assembled from 3 domains and are not covalently connected. The problem is that when i visualize the trajectories i observed that the protein domains are translated through the X axis and due to PBC, some domains appear from the other side of the membrane. I tried to use the PBCtools to reorient the protein to the center of the visualization cell but in vain.I tried this command: pbc wrap  -center origin -compound residue -all
And:
pbc wrap -centersel "protein" -center origin -compound residue -all
But none of them work even when I read the XST file using the readxst command
Any suggestions?
Regards, 
Marawan