Hi there!
I've played with the POL3 water model and discovered something odd.
I'm using a system with additional crystallographic water molecules. And no
matter what they are called in the pdb file, they are treated different
than the water molecules from the POL3BOX.
My tleap script is like this:
source leaprc.protein.ff14SB
loadoff solvents.lib
loadamberparams frcmod.pol3
loadoff atomic_ions.lib
loadamberparams frcmod.ionsjc_spce
WAT = PL3
prot = loadpdb protein_with_wat.pdb
solvateoct prot POL3BOX 10
addionsrand prot Cl- 0
savepdb prot protein_in_box.pdb
saveamberparm prot protein_in_box.prmtop protein_in_box.inpcrd
quit
And inside the protein_in_box.pdb I can see two 'types' of water molecules:
...
ATOM 5033 O WAT 325 7.134 20.787 8.832 1.00 0.00
ATOM 5034 H1 WAT 325 7.469 21.256 9.650 1.00 0.00
ATOM 5035 H2 WAT 325 6.134 20.818 8.817 1.00 0.00
TER
ATOM 5036 H1 WAT 326 3.741 -14.694 30.114 1.00 0.00
ATOM 5037 O WAT 326 2.785 -14.419 30.228 1.00 0.00
ATOM 5038 H2 WAT 326 2.634 -14.124 31.172 1.00 0.00
...
The first one is the crystallographic water, called WAT in the
protein_with_wat.pdb file, and the second is the water molecule from the
POL3BOX.
And it gets funny when I run a simulation for such a system. The
crystallographic water molecules barely move and the waters from the water
box are moving just fine. And that's why my system is blowing up after
minimisation.
So - how to fix it? Is my tleap script wrong somewhere?
Best regards,
Karolina
pt., 17 sty 2020 o 09:22 Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> napisał(a):
> 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 Sat Jan 18 2020 - 10:30:02 PST
