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 - 05:30:03 PDT
