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