From: Francesca Ricci-Tam (
Date: Thu May 06 2010 - 23:17:19 CDT

I am working with large pdb files with numerous residues, and I am trying to
find an automatic way to remove all hydrogens from these files, so that I do
not have to do it manually.
In a NAMD-L posting from a few years ago, I read that it could be done in
the following way with VMD:

mol load pdb your.pdb
set sel [atomselect top "not hydrogen"]
$sel writepdb new_noH.pdb

However, when I tried that with VMD, nothing happened.
The instructions aren't clear to me. For one thing, I do not know where I
need to save my pdb file ("your.pdb" in the above example) so that VMD will
be able to access it. Also, are those commands supposed to be typed in the
vmd command line in the exact format of those three lines?