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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 24 2018 - 06:00:02 PDT
