Hi all:
I would like to add Zn to the molecule before perform the MD simulations,
However, when I use the tleap to add ions, some error happened
the software vision is AMBER 11, and the force filed is leaprc.ff99bsc0
Here is the command
model=loadpdb xxx.pdb
addions model Zn 0
some error happened
addIons: Argument #1 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 fix this problem?
Thanks for your help
Yunjie Zhao
School of Physics
Huazhong University of Science and Technology
Wuhan, Hubei Province, China
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Received on Fri Oct 21 2011 - 06:00:04 PDT
