Issues with Gromacs Input Files

[fjclark]

Hello,

I'm running BSS version 2022.1.0, 8.g3f6b1c18 on linux, installed using conda. I'm attempting to run a short simulation with the gromacs input files supplied here. All relevant inputs/ notebooks are here.

I've run into a few issues:

1. Failure of getSystem(block=True). During equilibration steps (see bdr4_equilibration.ipynb) this command sometimes fails the first time it is run. However, it runs correctly the second time (without repeating the simulation). The system was also unexpectedly unstable (LINCS warnings) and exploded during "PMEMD NPT equilibration for 2ns without restraints" (Fatal error: 3 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.) . I had similar issues when using sander. The input was the ligand 1 complex for brd4.

2. Single point energy calculation works with Gromacs but fails with Amber (see gh_issue.ipynb). Error reads: "EXTRA POINTS: nnb too small!". Input was the ligand 1 complex for jnk1.

3. BSS fails to read Amber inputs generated with ParmEd (see bottom of gh_issue.ipynb). I converted the jnk1 input (ligand 1 complex) from gro/top to parm7/rst7 according to the discussion here. However, upon attempting to reload the parm7/rst files, I get [OSError: Failed to read molecules from ['jnk1_system.parm7', 'jnk1_system.rst7']. It looks like you failed to include a topology file.]()

Thanks very much.

[lohedges]

Hi there,

For part of question 1): I'm not sure why this happens but I've recently fixed this (last) week by simply re-trying the trjconv command if it happens to fail the first time. (Weirdly the failures only ever happen within getSystem() when calling a subprocesses, i.e. using the exact same commands on the command-line works every time!).

I should be able to check the other issues at some point tomorrow.

Cheers.

[fjclark]

Hi,

Thanks for the quick response. Great - I'll update to the latest version.

Cheers

[lohedges]

Out of interest, is there are reason why you need to use ParmEd to convert the GROMACS files, rather than using BioSImSpace directly, i.e.:

import BioSImSpace as BSS

# Load GROMACS system.
system = BSS.IO.readMolecules(["jnk1_complex.gro", "jnk1_complex.top"])

# Write to AMBER format.
BSS.IO.saveMolecules("test", system, ["prm7", "rst7"])

(This is what would be done behind the scenes if you loaded GROMACS files and tried to run a simulation with AMBER.)

This works, but the resulting topology file looks quite different to the one generated by ParmEd. A single-point calculation would test whether the information is self-consistent, despite the differences.

[fjclark]

The original issue I was having was instability during equilibration using sander through BSS and @jmichel80 mentioned that there had been issues previously with file conversion. To rule this out, I wanted to repeat the file conversion using ParmEd and re-run the equilibration to see if I got the same issues. Unfortunately I've not been able to run a single-point calculation using the BSS-converted files (see first part of see gh_issue.ipynb), or to load in the files produced by ParmEd to run a single-point calculation on those.

[lohedges]

Hi again,

I'm really not sure what's going on with those GROMACS files provided in the repository you linked to. Out of interest, I looked at their example notebook which shows how the files are generated. If I reproduce their code, but instead write to AMBER format files rather than GROMACS, then everything works, i.e. I can load back the files with BioSimSpace and I get the same results when performing single-point energy calculations with AMBER and GROMACS.

For reference, they are just parameterising the protein using FF14SB and "openff_unconstrained-2.0.0" for the ligand. It isn't possible to do this directly in BioSimSpace since the protein PDB contains missing atom types and the SDF file is required in order to provide the required stereochemistry information for the ligand.

Here's my script. (You'll just need to clone the abfe-benchmark repo to your working directory.)

import BioSimSpace as BSS

import parmed

from openff.toolkit.topology import Molecule
from openff.toolkit.typing.engines.smirnoff import ForceField as OFF_ForceField

try:
    from openmm import XmlSerializer, app, unit
    from openmm.app import HBonds, NoCutoff, PDBFile, ForceField
except ImportError:
    from simtk import unit
    from simtk.openmm import XmlSerializer, app
    from simtk.openmm.app import HBonds, NoCutoff, PDBFile

# Load in the ligand.
ligand_molecule = Molecule("abfe-benchmark/structures/jnk1/ligand1.sdf")

# Specify the "Sage" forcefield.
force_field = OFF_ForceField("openff_unconstrained-2.0.0.offxml")

# Parametrize the ligand molecule by creating a Topology object from it.
ligand_system = force_field.create_openmm_system(ligand_molecule.to_topology())

# Read in the coordinates of the ligand from the PDB file.
ligand_pdbfile = PDBFile("abfe-benchmark/structures/jnk1/ligand1.pdb")

# Convert the ligand system to a ParmEd object.
ligand_parmed_structure = parmed.openmm.load_topology(ligand_pdbfile.topology,
											          ligand_system,
											          ligand_pdbfile.positions)

# Write the ligand structure to AMBER format.
ligand_parmed_structure.save("ligand1.rst7", overwrite=True)
ligand_parmed_structure.save("ligand1.parm7", overwrite=True)

# Parse the protein PDB file.
protein_pdbfile = PDBFile("abfe-benchmark/structures/jnk1/protein.pdb")

# Load the AMBER protein force field through OpenMM.
omm_forcefield = app.ForceField("amber14/protein.ff14SB.xml", "amber14/tip3p.xml")

# Parameterize the protein.
protein_system = omm_forcefield.createSystem(protein_pdbfile.topology,
                                             nonbondedCutoff=1*unit.nanometer,
                                             nonbondedMethod=app.NoCutoff,
                                             constraints=None,
                                             rigidWater=False)

# Convert the protein System into a ParmEd Structure.
protein_parmed_structure = parmed.openmm.load_topology(
                                        protein_pdbfile.topology,
                                        protein_system,
                                        xyz=protein_pdbfile.positions)

# Write the protein structure to AMBER format.
protein_parmed_structure.save("protein.rst7", overwrite=True)
protein_parmed_structure.save("protein.parm7", overwrite=True)

# Load the ligand and protein with BioSimSpace.
ligand = BSS.IO.readMolecules("ligand1.*7")[0]
protein = BSS.IO.readMolecules("protein.*7")[0]

# Combine to form a complex.
complx = (ligand + protein).toSystem()

# Create a single-step minimisation protocol.
protocol = BSS.Protocol.Minimisation(steps=1)

# Create processes for AMBER and GROMACS simulations.
process_amb = BSS.Process.Amber(complx, protocol)
process_gmx = BSS.Process.Gromacs(complx, protocol)

# Modify the GROMACS config to perform zero steps.
config = process_gmx.getConfig()
config[1] = "nsteps = 0"
process_gmx.setConfig(config)

# Run the processes.
process_amb.start()
process_amb.wait()
process_gmx.start()
process_gmx.wait()

# Compare energies. (Where direct comparisons can be made.)
print(f"Bond energies... AMBER = {process_amb.getBondEnergy()}, GROMACS = {process_gmx.getBondEnergy()}")
print(f"Angle energies... AMBER = {process_amb.getAngleEnergy()}, GROMACS = {process_gmx.getAngleEnergy()}")
print(f"Dihedral energies... AMBER = {process_amb.getDihedralEnergy()}, GROMACS = {process_gmx.getDihedralEnergy()}")

This outputs:

Bond energies... AMBER = 202.0904 kcal/mol, GROMACS = 202.0662 kcal/mol
Angle energies... AMBER = 1111.9015 kcal/mol, GROMACS = 1111.8045 kcal/mol
Dihedral energies... AMBER = 4336.2379 kcal/mol, GROMACS = 4315.6788 kcal/mol

I'm not yet sure if the issue with the GROMACS files is our ability to read them, or whether they were invalid in the first place. I'll try to reproduce the above writing to GROMACS format, i.e. using the output of the script, rather what was uploaded to the benchmark repository.

Cheers.

[lohedges]

I've just re-run the above script, instead using ParmEd to write to GROMACS format. As you've found, on conversion to AMBER format within BioSimSpace, any AMBER simulation fails with the EXTRA POINTS: nnb too small!" message. While the GROMACS simulations work, the single point energies are different (but close) to those that I obtained above using the the AMBER files written by ParmEd. The output was as follows:

Bond energies... AMBER = None, GROMACS = 241.7304 kcal/mol
Angle energies... AMBER = None, GROMACS = 1124.9594 kcal/mol
Dihedral energies... AMBER = None, GROMACS = 4337.7390 kcal/mol

Given the inconsistencies, I'm not sure whether the issue is with ParmEd or us.

[jmichel80]

That's very helpful @lohedges ! @fjclark could you check whether the AMBER prm files produced by @lohedges 's script work with SOMD ? We can feedback to Bayer next week the above issues.

[fjclark]

Thanks very much @lohedges. @jmichel80 will do.

[fjclark]

@jmichel80 I can confirm that the AMBER files produced by @lohedges's script work with SOMD. However, test alchemical simulations crash when I use the same config file I'm using for my current work, giving "NaN or Inf has been generated along the simulation" during minimisation. This turned out to be due to the use of "constraint = allbonds". Do you have any suggestions as to why this is happening, given that the system appeared well equilibrated (I have used an equilibration scheme almost identical to the one which produced input which works with this config file).

All relevant input is here. I have:

-Produced AMBER format files for brd4, lig1 complex using @lohedges 's script (this failed at first due to this issue - despite having compatible versions of ParmEd and OpenMM in my environment, an incompatible version of ParmEd was bundled with AmberTools, which worked after manually modifying decorators.py).

-Equilibrated using pmemd and pmemd.cuda - see input.

-Run a short production run using SOMD through BSS - successful

-Run single alchemical windows using my standard config file with (failure) and without (success) constraint set to "allbonds".

Thanks

[jmichel80]

This is odd, constraints are disabled before energy minimisation. See https://github.com/michellab/Sire/blob/devel/wrapper/Tools/OpenMMMD.py#L1507-L1520

Also your single point energy before minimisation is identical before minimisation between the two runs, so I expect the same input was passed to integrator.minimiseEnergy()

Is the error reproducible ?

You could try disabling minimisation, that step may not be necessary for an ABFE run started from a structure equilibrated at discharge = 0.0

[fjclark]

I've repeated the calculations, only adding or removing "set_constraints = allbonds" to the config. Adding this consistently causes the simulations to crash during minimisation. I'm running my modified version of SOMD with Boresch restraints, but I've repeated this with the latest version of sire as contained within BSS-dev - I observe the same thing.

When disabling minimisation, I get:

  2 NaN or Inf has been generated along the simulation
  3 Starting /home/finlayclark/sire_boresch_2022.app/bin/somd-freenrg: number of threads equals 20
  4 srun: error: ishikawa: task 0: Exited with exit code 255

Very similar to with minimisation, only no output related to setting up the system is displayed.

[lohedges]

Out of interest, do the original GROMACS files work with SOMD? (For example, if you just perform minimisation and equilibration with GROMACS rather than PMEMD.) It would be interesting to know if you experience the same constraint related crashes with those, too.

[jmichel80]

Could you setup from scratch the input files with BioSimSpace (starting from pdb files extracted from the pmemd equilibration and solvating in BioSimSpace) to verify if SOMD runs without errors in that case ? If so comparing the prm7 files should indicate a discrepancy in the handling of bonded terms.

[fjclark]

@lohedges I'm not able to equilibrate the original GROMACS files in BSS using GROMACS - I get failures during my final NPT equilibration. Based on this, it seems likely that the issue is with the original files.