Problem creating topology for POPC using Interchange.from_smirnoff()

[dkchalmers]

Describe the bug

I am trying to create gromacs toppologies of lipid bilayers. However, using the function Interchange.from_smirnoff() fails when trying to make a topology for popc. This fails whether using a mol2 file, SMILES or IUPAC name as the input structure.

This process works correctly using cholesterol.

Error is: Warning: popc: Failed due to unspecified stereochemistry

I suspect the problem might be something to do with the phosphate group

To Reproduce

Run the attached script interchange2.ipynb
I have attached popc.mol2 and cholesterol.mol2

Output

Warning: popc: Failed due to unspecified stereochemistry

Computing environment (please complete the following information):
Linux opensuse 15.5

• Output of running conda list

packages in environment at /vcp1/people/david/bin/miniforge3/envs/openff:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
ambertools 23.6 cuda_None_nompi_py311h4a53416_105 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge
anyio 4.4.0 pyhd8ed1ab_0 conda-forge
apsw 3.46.0.1 py311h26bb8ec_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arpack 3.9.1 nompi_h77f6705_101 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
aws-c-auth 0.7.22 hbd3ac97_10 conda-forge
aws-c-cal 0.7.1 h87b94db_1 conda-forge
aws-c-common 0.9.23 h4ab18f5_0 conda-forge
aws-c-compression 0.2.18 he027950_7 conda-forge
aws-c-event-stream 0.4.2 h7671281_15 conda-forge
aws-c-http 0.8.2 he17ee6b_6 conda-forge
aws-c-io 0.14.10 h826b7d6_1 conda-forge
aws-c-mqtt 0.10.4 hcd6a914_8 conda-forge
aws-c-s3 0.6.0 h365ddd8_2 conda-forge
aws-c-sdkutils 0.1.16 he027950_3 conda-forge
aws-checksums 0.1.18 he027950_7 conda-forge
aws-crt-cpp 0.27.3 hda66527_2 conda-forge
aws-sdk-cpp 1.11.329 h46c3b66_9 conda-forge
azure-core-cpp 1.13.0 h935415a_0 conda-forge
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brotli-python 1.1.0 py311hb755f60_1 conda-forge
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comm 0.2.2 pyhd8ed1ab_0 conda-forge
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Additional context

Remove .txt to use...

cholesterol.mol2.txt
popc.mol2.txt
interchange2.ipynb.txt

[j-wags]

Hi @dkchalmers, I think this is actually working with both of your molecules, the issue with popc is just emitting a warning (not an error). We might see about squelching the warning, but I think your notebook is running successfully. Could you try using the outputs and let me know if there's an issue?

[dkchalmers]

Hi @j-wags. Ahh - thanks very much. I can see that it does indeed work. I was mislead by the warning and also that generating the topology for POPC takes 10 times as long as for cholesterol. I timed the two - cholesterol takes 35 seconds, popc takes 392 s.

[j-wags]

Hah, I saw a similar comment on related repo yesterday. Looks like it's already been deleted.

Thanks for the report. The long charge assignment time kinda makes sense since it's a large flexible molecule. We have a new AM1BCC charge assignment tool (NAGL) in the works that should be much faster, so hopefully the long parameterization time won't be a problem for much longer.

I'll close this issue since it seems like the POPC is being parameterized correctly, but please feel free to reopen it if you find further problems.

[dkchalmers]

Thanks for your reply - although I can generate a topology for a single POPC molecule, more than one seems to make things much slower - to the point that I cant generate a topology for a file containing 2 POPC molecules and 1 water.

The attached parameterise.py script works for a file containing 2 x cholesterol and 1 water

./paramaterise.py bilayer_c_solv.pdb
Making Topology
Reading Force Field
Assigning Force Field
Warning: Cannot perform Hydrogen sampling with GPU-Omega: GPU-Omega disabled.
Writing output files
Run time: 109.9 seconds

However the same thing with 2 x POPC and 1 water does not complete in > 2 hours

./paramaterise.py bilayer_p_solv.pdb
Making Topology
....

cholesterol.mol2.txt
bilayer_p_solv.pdb.txt
bilayer_c_solv.pdb.txt
popc.mol2.txt
paramaterise.py.txt

[j-wags]

Thanks for the example, I've reopened the issue and reproduced what you're seeing. The problem here appears to actually be in the Topology.from_pdb line. I think the long alkane chains make the template matching take forever because of all the symmetries.

Whole we work on fixing that, a quick workaround to your issue is to use the openmm.app.PDBFile object and the Topology.from_openmm API point.

import openmm.app
pdb = openmm.app.PDBFile("bilayer_p_solv.pdb")
top = Topology.from_openmm(pdb.topology, unique_molecules=[CHL, POPC, TIP3])

The downside to the Topology.from_openmm workaround is that it won't recognize proteins (that is, it can recognize whole unique molecules, but not proteins made of amino acids). So if your final topology was going to have a mix of proteins and lipids, you'd need to load the proteins using Topology.from_pdb, the lipids using Topology.from_openmm, and then combine them all using Topology.add_molecules.

(And again, I consider this failure of Topology.from_pdb to be a bug, and we'll work to resolve that so you don't need to use Topology.from_openmm moving forward)

[dkchalmers]

Thanks - a fix to this problem would be very helpful!

I tried to read my bilayer model using openmm.app.PDBFile - however, this does not work (error below). Although the error says 'attribute bonds', it seems to me that the 'pdb' object is missing bond-order information.

Script: parameterise.py.txt

./parameterise.py bilayer_p_solv.pdb
Reading components
Making Topology
Traceback (most recent call last):
File "parameterise.py", line 36, in
top = Topology.from_openmm(pdb, unique_molecules=[CHL, POPC, TIP3])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/david/bin/miniforge3/envs/openff/lib/python3.11/site-packages/openff/utilities/utilities.py", line 80, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "david/bin/miniforge3/envs/openff/lib/python3.11/site-packages/openff/toolkit/topology/topology.py", line 1410, in from_openmm
for omm_bond in openmm_topology.bonds():
^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'PDBFile' object has no attribute 'bonds'

[j-wags]

Change

Topology.from_openmm(pdb, unique_molecules=[CHL, POPC, TIP3])

to

Topology.from_openmm(pdb.topology, unique_molecules=[CHL, POPC, TIP3])

[dkchalmers]

Thanks for your help - that is working.

I am also very interested in working with peptides and proteins with lipid bilayers - so a fix for the original issue would be great.

[PEFrankel]

The stereochemistry warning is common, but you likely don't need to worry about it here. Although I cannot see, but as you suspect, the issue arises from the phosphate, which we've run into as well. allow_undefined_stereo=True quenches the warning. In my experience making molecules and interchanges, SDFs work well with from_file(). from_pdb() can be a little finicky (with a few lipids at least iirc).

In case you find it useful, this notebook parametrizes both a single lipid and/or a full PDB system (128 lipids fully hydrated here) in 10-15 min (note: this example implements HMR). Adjusting the molecule count and box size doesn't change the parametrization duration. Changing the charge assignment to NAGL instead of AM1BCC would make it faster as Jeff noted.