Re: [AMBER] Error adding OH⁻ ions in a simulation box

From: David A Case <>
Date: Tue, 22 Oct 2019 08:42:47 -0400

On Mon, Oct 21, 2019, Lucas Bandeira wrote:
>I'm trying to add NaOH in a water box. What I did was: I removed one
>hydrogen from the water pdb and used pdb4amber to "correct" it. I've also
>used antechamber to create OH⁻ óns parameters. However, I have the
>following warnings and errors:
>>>Unknown residue: OH number: 2676 type: Nonterminal

You are loading the PDB file before you have loaded the mol2 file that
defines the OH unit. Try putting the loadPdb command right before the
saveAmberParm command.


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Received on Tue Oct 22 2019 - 06:00:02 PDT
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