Thanks Matias and Carlos for your responses.
Yes, that's right, I didn't source the solvent.lib. I think, I managed to
generate a prmtop and inpcrd files for my system, but now I'm having
problem with running the simulation.
Out of curiosity, I just wanted to check, how the water model will affect
the protein itself and the water molecules behaviour. So I want to change
only the water model used in particular simulation and see what's happen.
In the Amber manual I've found an information, that PMEMD does not support
polarizable force fields, so I've changed to sander. I've also saw that I
need to include ipol=1 option.
I'm attaching my heat.in script. Am I missing something?
# 10ps equilibration with 1fs timestep Langevin dynamics
&cntrl
imin=0,
irest=0,
ntx=1,
ntb=1,
cut=10.0,
ntr=1,
ntc=2,
ntf=2,
tempi=0.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ig=1533,
nstlim=100000,
dt=0.001
ntpr=1000,
ntwx=500,
ntwr=500,
ntxo=2,
ioutfm=1,
ipol=1,
/
the rest of the system restraint
5
RES 1 310
END
END
Thanks again for your help!
Karolina
śr., 15 sty 2020 o 19:24 Carlos Simmerling <carlos.simmerling.gmail.com>
napisał(a):
> 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 Fri Jan 17 2020 - 00:30:02 PST
