Please show the cmds, including which ions frcmod file you loaded.
Bill
On 11/18/19 10:49 PM, 조준범 wrote:
> 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
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 18 2019 - 23:00:03 PST
