13 November 2024 1 7K Report

/home/hp/softwares/anaconda3/envs/AmberTools23/bin/teLeap: Fatal Error!

addIons: Argument #2 is of type String must be of type: [unit]

Here are some suggestions for correcting this error:

Verify the type of an argument with the desc command.

Check for alternate argument names with the list command.

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.

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