From: Joyce Tan (
Date: Tue Oct 19 2010 - 10:36:43 CDT


I have my 5000 frames .xtc and .gro loaded into vmd.

And I was trying to convert one of the frames into pdb through this:

set A [atomselect top protein frame 4998]
$A writepdb xx.pdb

When I load xx.pdb into the vmd, one atom from one residue is connected to
another atom from another residue. This particular bonding was not found in
the trajectory file. I really don't understand why is this happening. Can
someone help?