Closed yhgon closed 2 years ago
The error is exactly what it says. If you look in the PDB file you'll find the line
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
That means this model is a 1 A cube. That means the cutoff distance can't be more than 0.5 A. You tell it to use 1 nm (that is, 10 A).
I'm pretty sure that CRYST1 record is incorrect. The coordinates in the file span more than 1 A. But that's what the file says, so that's what it uses.
The second error is caused by the same problem:
fixer.addSolvent(fixer.topology.getUnitCellDimensions())
You tell it to add solvent, keeping the total size of the periodic box to the value loaded from the PDB file, that is, a 1 A cube. That doesn't give it room to actually add anything (including any neutralizing counterions). I would change that line to
fixer.addSolvent(padding=1*nanometer)
That will tell it to make sure there is at least 1 nm of water surrounding the solute on all sides.
thanks for your kind help. it works well.
Hi,
I want to make simulation pipeline from RCSB PDB file to OpenMM input with pdbfixer.
so I get get simple PDB file.
I check PDB file and it has only one chain and 56 residues.
when I try to get openMM system, I got error in PDB file with
OpenMMException: NonbondedForce: The cutoff distance cannot be greater than half the periodic box size.
so I try to fix PDB file with PDBFixer same as manual however I still have problem. how to fix this problem?
openMM and PDBFixer from conda-forge