Re: [AMBER] How to use polarizable water model in Amber 18?

From: Matias Machado <>
Date: Wed, 15 Jan 2020 13:46:11 -0300 (UYT)

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,


Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Karolina Mitusińska (Markowska)" <>
Para: "AMBER Mailing List" <>
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
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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