Hi,
I don't think the FF99sb force field has Zn ion parameters (you can
see what units are accessible after loading a leaprc file by typing
'list'). You would need to supply leap with a residue library file to
tell it how to create Zn ions.
-Dan
On Fri, Oct 21, 2011 at 8:37 AM, Yunjie Zhao <yjzhao.wh.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Oct 21 2011 - 11:00:03 PDT
