Re: how to remove all hydrogen atoms from PDB file?

From: J. Rui Rodrigues (
Date: Tue Apr 20 2004 - 09:01:20 CDT

You can do this easily with VMD:

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

Rui Rodrigues

Olya Kravchenko <> escreveu:

> Hi all! Is there any way to remove all hydrogen atoms from pdb file
> automatically? I've heard something called awk can do it...can somebody
> explain me how it works and how to use it? Thanks in advance!
> Olya

J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

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