AMBER Archive (2009)

Subject: Re: [AMBER] How to remove Hydrogen using ptraj

From: case (
Date: Tue Sep 01 2009 - 12:19:51 CDT

On Tue, Sep 01, 2009, Thomas Cheatham III wrote:
> strip @H*
> Note also that if you have 4-letter hydrogen names, typically the 4th
> character is wrapped so you might also want to add:
> strip @?H*

Is this true? Does ptraj not use the atom names in the prmtop file?

Fortunately, with pdb format version 3, there is no longer any "wrapping" of
hydrogen names in PDB files, so this problem should go away.


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