Re: [AMBER] Keeping input protein hydrogens?

From: David A Case <>
Date: Mon, 10 May 2021 16:58:28 -0400

On Mon, May 10, 2021, Markus Metz wrote:

>I am aware that it is recommended to remove any hydrogens from the original
>pdb file in order to prevent any naming issues.

This "recommendation" is only really relevant if you have hydrogens with bad
atom names. In some cases, it may be simpler to strip and regenerate them
than to figure out where the bad (non-IUPAC) names came from.

>Nevertheless, is there a way to keep the input hydrogens?

Amber won't strip hydrogens unless you explicitly ask it to do so, e.g. by
setting the --nohyd flag in pdb4amber (which is not the default).
(Running reduce will also change hydrogens, but again, you have to ask it to
do that.)

>I am planning to use amber for a ligand-protein complex minimization and
>would like to use a carefully prepared protein structure.

You should be fine: a "carefully prepared" protein structure ought to have
no problems with hydrogen names.


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Received on Mon May 10 2021 - 14:00:02 PDT
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