I also load the frcmod.ions~~~
This is the 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.
2019년 11월 19일 (화) 오후 3:45, 조준범 <j1300704.gmail.com>님이 작성:
> I add the line "source leaprc.water.spce", but same error occurs...
>
> 2019년 11월 19일 (화) 오후 3:17, Bill Ross <ross.cgl.ucsf.edu>님이 작성:
>
>> What params did you load for Li+? Typically there is an ions param
>> frcmod for each water model.
>>
>> Bill
>>
>> On 11/18/19 10:10 PM, 조준범 wrote:
>> > Hi, all.
>> >
>> > I'm trying to simulate ionic liquid system in AMBER18.
>> > I need to use Li+, so I tried to make the initial file with addIons
>> command
>> > in tleap.
>> >
>> > This is my script for tleap.
>> >
>> > source leaprc.gaff
>> > set default IPOL 1
>> > TFS = loadmol2 tfsi.mol2
>> > PYR = loadmol2 pyr14.mol2
>> > RTIL = loadPdb RTIL.pdb
>> > addIons RTIL Li+ 10 (This is the problem!!!!)
>> > loadamberparams frcmod.tfsi
>> > loadamberparams frcmod.pyr14
>> > setbox RTIL centers
>> > saveAmberParmPol RTIL RTIL.prmtop RTIL.inpcrd
>> >
>> > Any advice would be grateful :)
>> >
>> > p.s. I'm using modified parameters which is written in the frcmod.*
>> files.
>> > So you don't have to worry about that gaff is not for polarizable
>> > simulation.
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> *Junbeom Cho*
>
> Integrated Ph. D. Student
>
>
>
> Theoretical and Computational Soft Matters Laboratory
>
> School of Chemical and Biological Engineering
>
> Seoul National University
>
> 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
>
>
>
> Tel: +82-2-880-1529
>
> E-mail: cjb0704.snu.ac.kr
>
--
*Junbeom Cho*
Integrated Ph. D. Student
Theoretical and Computational Soft Matters Laboratory
School of Chemical and Biological Engineering
Seoul National University
1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
Tel: +82-2-880-1529
E-mail: cjb0704.snu.ac.kr
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Received on Mon Nov 18 2019 - 23:00:02 PST
