Hi,
Cu+ is not the unit name for the copper ion in Amber. You can check it in
atomic_ions.lib in the source files, or after loading the ion parameters
listing the unit names in tleap with "list". If I remember correctly, it
should be CU1. Could you try that?
Cheers,
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
El sáb, 28 ene 2023 a las 0:06, Scott Brozell via AMBER (<amber.ambermd.org>)
escribió:
> Hi,
>
> On Fri, Jan 27, 2023 at 06:12:51PM +0000, Gonzalo R. Vazquez-Jimenez via
> AMBER wrote:
> > I am trying to solvate and add metal ions to a pdb file. I am sourcing
> the appropriate force field and water model, loading the pdb file, and
> solvating it. I amm trying to add metal ions and appropriate counter ions
> and I am doing it with the indicated syntax of addIons [unit] [ Ion 1 ] [ #
> Ion 1 ] [ Ion 2 ] [ # Ion 2 ] . The command I am using for this is as
> shown:
> >
> >
> > addIons asyn Cu+ 10 Cl- 10
> >
> > However, when I do this, I get the following error message:
> >
> > Error: addIons: Argument #2 is type String must be of type: [unit]
> >
> > addIons unit ion1 #ion1 [ion2 #ion2]
> > UNIT _unit_
> > UNIT _ion1_
> > NUMBER _#ion1_
> > UNIT _ion2_
> > NUMBER _#ion2_
> > Adds counterions in a shell around _unit_ using a Coulombic potential
> > on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
> > opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
> > the specified numbers of _ion1_ [_ion2_] are added [in alternating
> order].
> > If solvent is present, it is ignored in the charge and steric
> calculations,
> > and if an ion has a steric conflict with a solvent molecule, the ion is
> > moved to the center of said molecule, and the latter is deleted. (To
> > avoid this behavior, either solvate _after_ addIons, or use addIons2.)
> > Ions must be monoatomic. Note that the one-at-a-time procedure is not
> > guaranteed to globally minimize the electrostatic energy. When
> neutralizing
> > regular-backbone nucleic acids, the first cations will generally be added
> > between phosphates, leaving the final two ions to be placed somewhere
> around
> > the middle of the molecule.
> > The default grid resolution is 1 Angstrom, extending from an inner radius
> > of (max ion size + max solute atom size) to an outer radius 4 Angstroms
> > beyond. A distance-dependent dielectric is used for speed
> >
> > How can I load these ions into my system if the appropriate syntax is
> not working?
>
> I can confirm that something appears to be amiss, eg,
> > source leaprc.protein.ff14SB
> > source leaprc.water.tip3p
> > x=loadpdb 1lgu.amber.pdb
> > addIons x Na+ 10 Cl- 10
> Adding 20 counter ions to "x" using 1A grid
> Total solute charge: 8.00 Max atom radius: 2.00
> ...
>
> while this fails as advertised:
> > addIons x Cu+ 10 Cl- 10
> Error: addIons: Argument #2 is type String must be of type: [unit]
> ...
>
> I didn't investigate further. Hopefully, the originators of Cu+ can help.
>
> scott
>
>
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Received on Fri Jan 27 2023 - 21:00:02 PST
