Dear Matias and David,
Thank you for your replies. But, how can I set those parameters for OH⁻? Do
I have to use Antechamber?
Sincerely,
Lucas Bandeira
On Thu, Oct 17, 2019 at 10:21 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Lucas,
>
> The warning/error messages are very clear:
>
> 1)
> -----
> 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
>
> 2)
> -----
> 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.
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Lucas Bandeira" <bandeiralucas97.gmail.com>
> Para: "David Case" <david.case.rutgers.edu>
> CC: amber.ambermd.org
> 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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> >
>
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Received on Fri Oct 18 2019 - 11:00:02 PDT
