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?
Thank you,
Gonzalo Vazquez
This email may contain proprietary, confidential and/or privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender by reply email and delete all copies of this message.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 27 2023 - 10:30:02 PST
