It isn't clear they one would want to use a polarizable water model with a
non polarizable protein model (ff14SB). Make sure you know what you want to
do here.
On Wed, Jan 15, 2020, 12:46 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Karolina,
>
> You aren't loading the library that contains the unit POL3BOX, which is
> "solvents.lib"
>
> Such library is loaded when fist sourcing a cmd file of a water model (for
> example: leaprc.water.tip3p)
>
> Best regards,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Karolina Mitusińska (Markowska)" <markowska.kar.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Miércoles, 15 de Enero 2020 10:39:39
> Asunto: [AMBER] How to use polarizable water model in Amber 18?
>
> Dear Amber users,
>
> I was trying to use the polarizable water model, POL3, which according to
> the manual should be included in the $AMBERHOME/dat/leap/cmd as
> leaprc.water.pol3 and used in tleap script as source leaprc.water.pol3.
> Unfortunately, it is not present in that directory. I'm using Amber18.
>
> I've found it in $AMBERHOME/dat/leap/parm as frcmod.pol3 and used it in my
> script, but it is still not working.
>
> source leaprc.protein.ff14SB
> loadamberparams frcmod.pol3
> HOH = PL3
> prot = loadpdb protein.pdb
> solvateoct prot POL3BOX 10
>
> I tried to use the above script, but I got error:
>
> /usr/local/src/amber18/bin/teLeap: Fatal Error!
> solvateOct: Argument #2 is type String must be of type: [unit]
> usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
>
> Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
>
> What should I do to use the POL3 water model? Which frcmod file for ions
> should I use with the POL3 water model?
> And can I use it with the leaprc.protein.ff14SB force field?
>
> Thanks for your help!
> Best regards,
> Karolina Mitusińska
> PhD student
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Received on Wed Jan 15 2020 - 10:30:02 PST
