From: Subbarao Kanchi (
Date: Thu Jun 13 2013 - 11:24:21 CDT

Hi anurag and john,
                           I face this problem long back. solution is very
easy. If you merge *file1* (.psf .pdb) and* file2* (.psf .pdb) in VMD, you
will get *merged.psf* and *merged.pdb*. The problem is that CA atom
coordinates becomes (0 0 0) that is why structure seems to be corrupted.
The solution that I find for this problem is you can mix the two .pdb files
by the command "cat" in LINUX terminal.
                           i.e *cat file1.pdb file2.pdb > merged.pdb*

Then remove the intermediate text lines in between two files in the *
merged.pdb* and later load in VMD along with *merged.psf*
you can save coordinates *merged.pdb *again to get the correct
(continuous) index numbers for atoms.