ok. You'll still need to specify which water model you want to use for the
water in the pdb file. You also need to set up a periodic system. The
details of that will depend on the previous MD simulation. That will
determine what type of box is needed, and the dimensions. It's possible to
do but might take some work that isn't automated. Look for instances of
"setbox" in the Amber 18 manual, and also you can do a search for setbox in
the mailing list archive on ambermd.org.
On Thu, May 24, 2018 at 9:07 AM, Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> 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 - 07:00:02 PDT
