I believe 'loadamberparams frcmod.ions1lm_1264_spce' just loads the
params for Li+, but you also have to loadoff some.lib I think to get the
model specifying the atom, naming the atom name for the pdb match and
the type, which is defined in the frcmod. Look for a tutorial maybe.
Bill
before addIons - apparently it isn't being loaded by '
On 11/18/19 11:09 PM, 조준범 wrote:
> Commands and error messages are below.
> And frcmod.ions1lm_1264_spce is copied from $AMBERHOME/dat/leap/parm/ to
> work directory.
>
> < tleap commands >
>
> source leaprc.gaff
> source leaprc.water.spce
> set default IPOL 1
> TFS = loadmol2 tfsi.mol2
> PYR = loadmol2 pyr14.mol2
> RTIL = loadPdb RTIL.pdb
> loadamberparams frcmod.tfsi
> loadamberparams frcmod.pyr14
> loadamberparams frcmod.ions1lm_1264_spce
> addIons RTIL Li+ 10
> setbox RTIL centers
> saveAmberParmPol RTIL ../RTIL.prmtop RTIL.inpcrd
>
> < Error message >
>
> /home/cleartimes24/amber18/bin/teLeap: Fatal 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.
>
> Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Nov 18 2019 - 23:30:02 PST
