From: Ajasja Ljubetič (
Date: Fri May 07 2010 - 02:45:30 CDT

Use Extensions->TkConsole to open the console and paste the commands there.
For the pdb file: you either have to specify the whole path or use the cd
command to change to the directory where your pdbs are located.
You can check the current directory by typing pwd to the TkConsole.
Perhaps you would also like to check out


On Fri, May 7, 2010 at 06:17, Francesca Ricci-Tam <>wrote:

> 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?