Re: [AMBER] Adding OH- to a water box

From: Matias Machado <>
Date: Thu, 17 Oct 2019 10:20:19 -0300 (UYT)

Dear Lucas,

The warning/error messages are very clear:

Created a new atom named: Na within residue: .R<NA 2665>
  Added missing heavy atom: .R<NA 2665>.A<NA 1>

FATAL: Atom .R<NA 2665>.A<Na 2> does not have a type.

The atom name for NA residue is "NA" (yes, the same name as the residue), not "Na"... that's way Leap "Added missing heavy atom".

Check $AMBERHOME/dat/leap/lib/atomic_ions.lib

Unknown residue: OH number: 2687 type: Nonterminal

Creating new UNIT for residue: OH sequence: 2687
Created a new atom named: O within residue: .R<OH 2687>

FATAL: Atom .R<OH 2687>.A<O 1> does not have a type.

You aren't loading any parameter for OH.



----- Mensaje original -----
De: "Lucas Bandeira" <>
Para: "David Case" <>
Enviados: Domingo, 13 de Octubre 2019 14:50:48
Asunto: Re: [AMBER] Adding OH- to a water box

On Sat, Oct 12, 2019, Lucas Bandeira wrote:
> > Why is it not as easy as adding water with AddToBox? You just define a
> > PDB file with two atoms (for the OH molecule), and use AddToBox in the
> > usual way. I do that all the time for molecule ions.
> But what about the overall negative charge in the OH⁻? It will be add
> automatically?

> AddToBox just uses size considerations, and doesn't try to evaluate
> electrostatics. The charges on the atoms will be in the unit you create
> (usually in mol2 format, but possibly in prep or off formats) that you
> will then load into tleap.

I'm trying to add OH⁻ in a water box, but I can't generate the .inpcrd and
.prmtop. I'm sending in attachment the files I'm using and the file with
the output that I get.

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Received on Thu Oct 17 2019 - 06:30:03 PDT
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