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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>
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Received on Thu May 24 2018 - 05:30:04 PDT
