Error in alignment of reference PDB

[Sky Jin]

Dear all,

I want to do a targeted MD simulation based on RMSD in openMM-plumed. I write a python code like below:

from simtk.openmm.app import *

from simtk.openmm import *

from simtk.unit import *

from sys import stdout

import openmmplumed

from openmmplumed import PlumedForce

pdb = PDBFile('6n7n_modeller_final.pdb')

forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')

system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff,

        nonbondedCutoff=1*nanometer, constraints=HBonds)

tmd_script = """

rmsd: RMSD REFERENCE=6n7t_modeller_final.pdb TYPE=OPTIMAL

RESTRAINT ARG=rmsd AT=0 KAPPA=150.0 LABEL=restraint

PRINT ARG=restraint.bias,t FILE=COLVAR

ENDPLUMED

"""

system.addForce(PlumedForce(tmd_script))

integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)

platform = Platform.getPlatformByName('OpenCL')

simulation = Simulation(pdb.topology, system, integrator, platform)

simulation.context.setPositions(pdb.positions)

simulation.minimizeEnergy()

simulation.reporters.append(PDBReporter('output.pdb', 1000))

simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,

        potentialEnergy=True, temperature=True))

simulation.step(50000)

The reference pdb "6n7t_modeller_final.pdb" has same atoms to the system "6n7n_modeller_final.pdb". But I get a problem like below:

Exception: 

+++ PLUMED error

+++ at SingleDomainRMSD.cpp:39, function void PLMD::SingleDomainRMSD::readReference(const PLMD::PDB&)

+++ assertion failed: wd>epsilon

+++ message follows +++

It looks like weights used for displacement are zero. Check your reference PDB file.

Could anyone give some suggestions on how to fix this? I tried to search this error in the Google group but get no useful information.

Best wishes,
Shikai

[Sky Jin]

Sorry I found the issue. Based on this page https://www.plumed.org/doc-v2.6/user-doc/html/pdbreader.html, the b-factor and occupancy of the atoms should be 1. I use modeller generated file so both of them are 0.

Best,