I'm a little confused about what you're trying to simulate. Is there
already water in the system? Are you simulating a periodic system (solution
phase) , or a molecule in the gas phase with some water included? If the
latter, you would tell the MD module that it is not periodic. If the
former, you need to add a box defining the volume, and possibly (likely)
add water to completely fill this box unless your initial coordinates
already do this.
On Thu, May 24, 2018, 8:53 AM Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> Dear Carlos,
>
> I've added
>
> loadamberparams frcmod.tip3pf
>
> to my tleap script (Amber14), but the simulation still crashes.
>
> I tried to use the solvateOct command, but it gives me another layer(?) of
> water molecules outside of my complete PDB in which I don't want to change
> the amount of water molecules and so on.
> I've typed
>
> solvateoct prot TIP3PBOX 0.0
>
> and got more waters. And this is not what I wanted.
> Is there a way to tell tleap about the water model without using the
> solvateoct command (or make it not to add those waters?)?
>
> 2018-05-24 14:17 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com
> >:
>
> > you haven't told leap that you want to solvate your system in water,
> which
> > water model to use, and how much.
> > Look in the Amber 18 manual, section 3.5 "Solvents", and 13.6.40.
> > "solvateBox and solvateOct". also look at the tutorials on the
> ambermd.org
> > site.
> >
> > On Thu, May 24, 2018 at 8:07 AM, Karolina Mitusińska (Markowska) <
> > markowska.kar.gmail.com> wrote:
> >
> > > Dear Amber Users,
> > >
> > > I want to run a simulation of a protein-ligand complex immersed in
> > water. I
> > > have a complete PDB file and I only want to generate the topology
> > (.prmtop)
> > > and coordinates (.inpcrd) files.
> > >
> > > I've tried:
> > > source leaprc.ff14SB
> > > loadamberparams frcmod.ionsjc_tip3p
> > > loadamberparams ../TSO.frcmod
> > > loadoff ../TSO.lib
> > >
> > > prot = loadpdb complete_pdb.pdb
> > >
> > > check prot
> > > charge prot
> > >
> > > saveamberparm prot complete_pdb.prmtop complete_pdb.inpcrd
> > > quit
> > >
> > > but then my simulation did not start and PMEMD gave me an error that
> say:
> > > ERROR: Box parameters not found in inpcrd file!
> > >
> > > So I modified my tleap script
> > > source leaprc.ff14SB
> > > loadamberparams frcmod.ionsjc_tip3p
> > > loadamberparams ../TSO.frcmod
> > > loadoff ../TSO.lib
> > >
> > > prot = loadpdb complete_pdb.pdb
> > >
> > > check prot
> > > charge prot
> > > setbox prot vdw
> > >
> > > saveamberparm prot complete_pdb.prmtop complete_pdb.inpcrd
> > > quit
> > >
> > > And now my simulation crashes during equilibration step with a longer
> > error
> > > message:
> > > ERROR: Calculation halted. Periodic box dimensions have changed too
> much
> > > from their initial values.
> > > Your system density has likely changed by a large amount, probably
> from
> > > starting the simulation from a structure a long way from equilibrium.
> > >
> > > [Although this error can also occur if the simulation has blown up
> for
> > > some reason]
> > >
> > > The GPU code does not automatically reorganize grid cells and thus
> you
> > > will need to restart the calculation from the previous restart file.
> > > This will generate new grid cells and allow the calculation to
> > continue.
> > > It may be necessary to repeat this restarting multiple times if your
> > > system
> > > is a long way from an equilibrated density.
> > >
> > > Alternatively you can run with the CPU code until the density has
> > > converged
> > > and then switch back to the GPU code.
> > >
> > > And although I find that message quite informative, I don't know how to
> > > manage with my simulation.
> > >
> > > I'm using pmemd.CUDA for all simulations steps, I've tried to run some
> of
> > > them using the regular pmemd, but I'm still having the same error.
> > >
> > > Could this error be related with the preparation of the PDB file?
> > > How should I prepare my complete PDB file?
> > >
> > > Many thanks for your help!
> > > Karolina Mitusińska
> > > PhD student
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > AMBER.ambermd.org
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> >
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Received on Thu May 24 2018 - 06:00:03 PDT
