Relative Free Energy of solvation

[mathilfiker]

Dear developers,

Thank you for your work and your dedication.
I'm trying to calculate the relative free energy of solvation of two molecules. They are the same molecules but with different sets of charges. I tried following your RBFE tutorial but neglected the protein. The transformation is correctly created and the calculations run, but the RFE results to be zero. Do you have any suggestions on how to tackle this problem?

Best wishes,
Mathias

[IAlibay]

Hi @mathilfiker,

Could you provide more details about how you did your rhfe calculation?

I.e. did you calculate both a vacuum and solvent leg? What were your components for the end states of each calculation?

[mathilfiker]

Hello @IAlibay ,
As a first attempt, I followed the tutorial. Specifically, calling LigandA the molecule with the set of charges A, and LigandB the molecule with set of charges B, I did:

ligands = [ligandA,ligandB]
ligand_network = network_planner(
    ligands=ligands,
    mappers=[mapper],
    scorer=scorer
)
mapping = next(iter(ligand_network.edges))
solvent = openfe.SolventComponent()
systemA = openfe.ChemicalSystem({
    'ligand': mapping.componentA,
    'solvent': solvent
})
systemB = openfe.ChemicalSystem({
    'ligand': mapping.componentB,
    'solvent': solvent
})
protocol = RelativeHybridTopologyProtocol(settings)
transformation = openfe.Transformation(
    systemA,
    systemB,
    protocol,
    mapping={'ligand': mapping},
)
transformations = []
for mapping in ligand_network.edges:
    for leg in ['solvent']:#, 'complex']:
        sysA_dict = {'ligand': mapping.componentA,
                     'solvent': solvent}
        sysB_dict = {'ligand': mapping.componentB,
                     'solvent': solvent}
        # The following is copy and pasted from the tutorial, but since I commented 'complex' in the for loop it shouldn't be considered
        if leg == 'complex':
            sysA_dict['protein'] = protein
            sysB_dict['protein'] = protein
        sysA = openfe.ChemicalSystem(sysA_dict, name=f"{mapping.componentA.name}_{leg}")
        sysB = openfe.ChemicalSystem(sysB_dict, name=f"{mapping.componentB.name}_{leg}")

        prefix = "easy_rbfe_" 

        transformation = openfe.Transformation(
            stateA=sysA,
            stateB=sysB,
            mapping={'ligand': mapping},
            protocol=protocol,  # use protocol created above
            name=f"{prefix}{sysA.name}_{sysB.name}"
        )
        transformations.append(transformation)

network = openfe.AlchemicalNetwork(transformations)

Maybe there is something I didn't understand from the tutorial, so any input can be useful :).

Best,
Mathias

[IAlibay]

So there's two separate issues I can see here:

1. The solvent transformation is giving a dG of 0 with different charges.
2. The hydration free energy calculation is missing a vacuum leg.

Issue 1

This will need more information:

• How are you feeding in the partial charges?
• What version of openfe & gufe do you have installed?

Issue 2

In order to do a relative hydration free energy calculation, you will need a vacuum transformation.

This should be something like:

ligands = [ligandA,ligandB]
ligand_network = network_planner(
    ligands=ligands,
    mappers=[mapper],
    scorer=scorer
)

# Create your settings
solvent_settings = RelativeHybridTopologyProtocol.default_settings()
vacuum_settings = RelativeHybridTopologyProtocol.default_settings()
vacuum_settings.forcefield_settings.nonbonded_method = "nocutoff" 

# Create the Protocol objects
protocols = {
    'solvent': RelativeHybridTopologyProtocol(solvent_settings),
    'vacuum': RelativeHybridTopologyProtocol(vacuum_settings)
}

transformations = []
for mapping in ligand_network.edges:
    for leg in ['solvent', 'vacuum']:
        sysA_dict = {'ligand': mapping.componentA,}
        sysB_dict = {'ligand': mapping.componentB,}
        if leg == 'solvent':
            sysA_dict['solvent'] = solvent
            sysB_dict['solvent'] = solvent

        sysA = openfe.ChemicalSystem(sysA_dict, name=f"{mapping.componentA.name}_{leg}")
        sysB = openfe.ChemicalSystem(sysB_dict, name=f"{mapping.componentB.name}_{leg}")

        transformation = openfe.Transformation(
            stateA=sysA,
            stateB=sysB,
            mapping={'ligand': mapping},
            protocol=protocols[leg]
            name=f"{sysA.name}_{sysB.name}_{leg}"
        )
        transformations.append(transformation)

network = openfe.AlchemicalNetwork(transformations)

By calculating both the vacuum and solvent transformation, you can then take their difference to get the ddG of hydration.

[mathilfiker]

Hello, I tried adding the vacuum leg to the simulation, but both the transformations return a dG of zero. The way I feed partial charges is the following:

chgsA = np.load('chargesA.npy')
sdf_file = 'path_to_file.sdf'
suppl = Chem.SDMolSupplier(sdf_file.removeHs=False)
off_molecule = Molecule.from_rdkit(suppl[0])
ureg = UnitRegistry()
off_molecule.partial_charges = Quantity(chgsA,unit.elementary_charge)
ligandA = openfe.SmallMoleculeComponent.from_openff(off_molecule)

This method proved successful when I computed ABHFEs.

[IAlibay]

This is rather odd - could you tell us what your python environment looks like @mathilfiker ? Something like mamba list or conda list

[mathilfiker]

This is the list of all installed packages:

# packages in environment at openfe_env_2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
adjusttext                1.3.0              pyhd8ed1ab_0    conda-forge
amberlite                 22.0                     pypi_0    pypi
ambertools                22.5            py310hd182041_0    conda-forge
amberutils                21.0                     pypi_0    pypi
annotated-types           0.7.0              pyhd8ed1ab_0    conda-forge
anyio                     4.6.2.post1        pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310ha75aee5_5    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               h04ea711_2    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
babel                     2.16.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
biopython                 1.84            py310hc51659f_0    conda-forge
bleach                    6.2.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.6               hef167b5_0    conda-forge
boost                     1.78.0          py310hcb52e73_5    conda-forge
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0           py310hf71b8c6_2    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.3               hb9d3cd8_1    conda-forge
c-blosc2                  2.15.2               h68e2383_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.5.0              pyhd8ed1ab_0    conda-forge
cairo                     1.18.0               hbb29018_2    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py310h8deb56e_0    conda-forge
cftime                    1.6.4           py310hf462985_1    conda-forge
chardet                   5.2.0           py310hff52083_2    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
cinnabar                  0.4.1              pyhd8ed1ab_1    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
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cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.11          py310h5b1441d_3    conda-forge
debugpy                   1.8.9           py310hf71b8c6_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
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executing                 2.1.0              pyhd8ed1ab_0    conda-forge
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gdk-pixbuf                2.42.12              hb9ae30d_0    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
graphviz                  12.0.0               hba01fac_0    conda-forge
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gsd                       3.4.2           py310ha75aee5_0    conda-forge
gtk2                      2.24.33              h6470451_5    conda-forge
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gufe                      1.1.0              pyhd8ed1ab_1    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
harfbuzz                  9.0.0                hfac3d4d_0    conda-forge
hdf4                      4.2.15               h2a13503_7    conda-forge
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ipython                   8.30.0             pyh707e725_0    conda-forge
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json5                     0.10.0             pyhd8ed1ab_0    conda-forge
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jsonschema-specifications 2024.10.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
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krb5                      1.21.3               h659f571_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libblas                   3.9.0           25_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
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libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcblas                  3.9.0           25_linux64_openblas    conda-forge
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libdeflate                1.22                 hb9d3cd8_0    conda-forge
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libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgd                     2.3.3                h119a65a_9    conda-forge
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liblapack                 3.9.0           25_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libnetcdf                 4.9.2           nompi_h2564987_115    conda-forge
libnghttp2                1.64.0               h161d5f1_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
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libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsqlite                 3.47.0               hadc24fc_1    conda-forge
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libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libtiff                   4.7.0                he137b08_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.4.0                h2c329e2_0    conda-forge
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libxcb                    1.17.0               h8a09558_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               h4c95cb1_3    conda-forge
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libzip                    1.11.2               h6991a6a_0    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
llvmlite                  0.43.0          py310h1a6248f_1    conda-forge
lomap2                    3.1.0              pyhff2d567_0    conda-forge
lxml                      5.3.0           py310h6ee67d5_2    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
markupsafe                3.0.2           py310h89163eb_0    conda-forge
matplotlib-base           3.9.2           py310h68603db_2    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge
mdanalysis                2.1.0           py310h769672d_4    conda-forge
mdtraj                    1.10.1          py310he1cc299_1    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mmtf-python               1.1.3              pyhd8ed1ab_0    conda-forge
mpiplus                   v0.0.2             pyhd8ed1ab_0    conda-forge
mrcfile                   1.5.3              pyhd8ed1ab_0    conda-forge
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nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_ha5d1325_107    conda-forge
netcdf4                   1.7.2           nompi_py310h5146f0f_100    conda-forge
networkx                  3.4.2              pyh267e887_2    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  7.2.2              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numba                     0.60.0          py310h5dc88bb_0    conda-forge
numexpr                   2.10.2          py310hdb6e06b_100    conda-forge
numpy                     1.26.4          py310hb13e2d6_0    conda-forge
ocl-icd                   2.3.2                hb9d3cd8_2    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
opencl-headers            2024.10.24           h5888daf_0    conda-forge
openfe                    1.2.0              pyhd8ed1ab_0    conda-forge
openfe-analysis           0.2.0              pyhd8ed1ab_0    conda-forge
openff-amber-ff-ports     0.0.4              pyhca7485f_0    conda-forge
openff-forcefields        2024.09.0          pyhff2d567_0    conda-forge
openff-interchange        0.4.0              pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.4.0              pyhd8ed1ab_0    conda-forge
openff-models             0.1.2              pyhca7485f_0    conda-forge
openff-toolkit            0.16.6             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.16.6             pyhd8ed1ab_0    conda-forge
openff-units              0.2.2              pyhca7485f_0    conda-forge
openff-utilities          0.1.12             pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.2                h488ebb8_0    conda-forge
openmm                    8.1.2           py310h6b72300_2    conda-forge
openmmforcefields         0.12.0             pyhd8ed1ab_0    conda-forge
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openssl                   3.4.0                hb9d3cd8_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.2               pyhff2d567_1    conda-forge
packmol                   20.15.1              hc8b2c43_1    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    2.2.2           py310hf9f9076_1    conda-forge
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pip                       24.3.1             pyh8b19718_0    conda-forge
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py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
py3dmol                   2.4.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.27.0          py310h25ff670_0    conda-forge
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pydantic-core             2.27.1          py310h505e2c1_0    conda-forge
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python-fastjsonschema     2.21.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    5_cp310    conda-forge
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pyzmq                     26.2.0          py310h71f11fc_3    conda-forge
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sander                    22.0                     pypi_0    pypi
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scipy                     1.14.1          py310hfcf56fc_1    conda-forge
seaborn                   0.13.2               hd8ed1ab_2    conda-forge
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setuptools                75.6.0             pyhff2d567_1    conda-forge
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[hannahbaumann]

Hi @mathilfiker , thank you for sending this along!
I'm also not sure yet what might be going on, but if you have some time, could you maybe check the following things?

• Are there any warnings or errors in the simulation .log file?
• What are the output files of the simulation? Does the shared_XXX folder contain a simulation_real_time_analysis.yaml file? That file should contain the calculated DG values (and errors) after different simulation lengths, e.g. after 1 ns, 2 ns, ..., depending on the overall length of the simulation. Are all DG estimates in that file zero as well? Are the uncertainties zero too?
• Do the ligands (the two variants of the same ligand) have the same name? You can check that by printing ligandA.name of the SmallMoleculeComponent
• Could you print the partial charges for both ligands, starting e.g. from the SmallMoleculeComponent, and verify that the partial charges are different and as expected? E.g. printing ligandA.to_openff().partial_charges
• The partial charges that are being used in the actual simulation are also present in the db.json file in the shared_XXX directory. That could be a another thing to check if those are as expected.

Please let me know if you have any questions!

[mathilfiker]

Hi @hannahbaumann, thank you for answering!

• There are no errors nor warnings in the .log file

• All DGs and uncertainties are zero
  - ligandA.name shows a different name than ligandB.name

• Partial charges printed with ligandA.to_openff().partial_charges are actually different for the two ligands

• The db.json file only shows details for one ligand, so I don't know about the other. Its structure is
  {
  "gaff-2.11": {
  "1": {
  "ffxml": # force field parameters for ligandA
  "smiles": # SMILES for ligand A
  }
  }
  }

Is this .db file supposed to look like this?

[hannahbaumann]

Thanks @mathilfiker !

Yes, that's how the db.json would look like, the charges should be in the ffxml, maybe you could just check it for the first ligand atom?

All DGs and uncertainties are zero

That's very odd indeed! Just to clarify, this is from the simulation_real_time_analysis.yaml file or from the resuls .json file?

[mathilfiker]

Where should I find the ffxml? it is not in the working directory.

Yes, the DGs = 0 come from simulation_real_time_analysis.yaml

[hannahbaumann]

Thanks @mathilfiker ! This is indeed very weird!
The ffxml file should be in the shared_XXX folder.

We will try to replicate this issue on our end to see whether there could be a bug somewhere. Apologies for the delays on this!

[atravitz]

@mathilfiker - could you clarify if within simulation_real_time analysis.yaml you are seeing standard_error_in_kT: 0.0, or if it is a very small value (on the order of 1e-11)?

[IAlibay]

Hi @mathilfiker just a brief update, it looks like this is a legitimate (albeit obscure) bug in the way we parameterize our systems.

You can see a very messy bugfix for it here: #1116

FIxing it properly is going to require some rework of some of our Protocol internals and a lot of validation, so we need to discuss things internally (probably next week) before we move forward with this.

If you want to try out completly experimental code, then that bugfix may work.