Re: [AMBER] LEaP Issue

From: Scott Brozell via AMBER <>
Date: Fri, 27 Jan 2023 22:04:31 -0500


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.


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Received on Fri Jan 27 2023 - 19:30:02 PST
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