I’m sorry, I did not read the complete message and missed that you’d already corrected for this initial error.
// Gustaf
> On 24 May 2018, at 14:07, 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 - 05:30:04 PDT
