Protein+Membranes.ipynb | Parameters to generate the topology

[Saul Flores]

Hello, I encounter this error when trying to generate the topology:

OpenMMException                           Traceback (most recent call last)
<ipython-input-10-2da7178e01ab> in <cell line: 69>()
     67 
     68 # solvate it in 0.15 M NaCl solution
---> 69 modeller.addMembrane(
     70     forcefield,
     71     lipidType=membrane,

1 frames
/usr/local/lib/python3.10/site-packages/openmm/app/modeller.py in addMembrane(self, forcefield, lipidType, membraneCenterZ, minimumPadding, positiveIon, negativeIon, ionicStrength, neutralize, residueTemplates)
   1536                     mergedPositions[j+numMembraneParticles] = (weight1*proteinPos[j] + weight2*scaledProteinPos[j])
   1537             context.setPositions(mergedPositions)
-> 1538             integrator.step(20)
   1539 
   1540         # Add the membrane to the protein.

/usr/local/lib/python3.10/site-packages/openmm/openmm.py in step(self, steps)
   6860             the number of time steps to take
   6861         """
-> 6862         return _openmm.LangevinIntegrator_step(self, steps)
   6863 
   6864     def __init__(self, *args):

OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan

First this happened after 20 minutes of running. The second time, I increased the patch size to 1.5 and it gave the same error after 45 minutes of running. The protein I am using is from the OPM database and I can visualize it correctly.

Any help would be appreciated in trying to go forward with topology generation.

[Pablo Ricardo Arantes]

I will check and back to you.