AMBER Archive (2009)

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

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Sep 01 2009 - 10:55:43 CDT

> I would like to remove hydrogen from the trajectory before converting into PDB.
> But I could not remove hydrogen using strip :H or strip :H*
> When using strip :H
> none of the hydrogen where removed
> when using strip :H*
> only 34 not all the hydrogen were removed.

":" is the designator for a residue name; "@" is for an atom name so you
want:

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*

-tec3


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