Ok, sorry for not being clear about the completeness of the PDB file.
The PDB file consists of protein, ligand, water molecules and additional
ions. It is a periodic system in which I don't want to add more water
molecules.
I did some modifications to a previously used file from MD simulation and I
want to use it again for another simulation.
Is it somehow possible? :)
2018-05-24 14:56 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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
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Received on Thu May 24 2018 - 06:30:03 PDT
