I have attempted to use openff-toolkit generate files as inputs for the ligand_tutorial. The atomMapping finished without error, but, during the makeHybrid component, I get this error in my log file:
"
ligandHybridTop__log_> Constructing dummies…
ligandHybridTop__log_> Dummies in stateA:
ligandHybridTop__log_> Dummy…: 51 DUM_MOL0_24 | 0.00 | 12.01 → MOL0_24 | -0.18 | 12.01
ligandHybridTop__log_> Dummy…: 52 DUM_MOL0_27 | 0.00 | 12.01 → MOL0_27 | 0.11 | 12.01
ligandHybridTop__log_> Dummy…: 53 DUM_MOL0_51 | 0.00 | 1.01 → MOL0_51 | 0.05 | 1.01
ligandHybridTop__log_> Dummy…: 54 DUM_MOL0_52 | 0.00 | 1.01 → MOL0_52 | 0.05 | 1.01
ligandHybridTop__log_> Dummy…: 55 DUM_MOL0_53 | 0.00 | 1.01 → MOL0_53 | 0.05 | 1.01
ligandHybridTop__log_> Dummies in stateB:
ligandHybridTop__log_> Dummy…: 48 MOL0_47 | 0.13 | 1.01 → DUM_MOL0_47 | 0.00 | 1.01
ligandHybridTop__log_> Construct bonds…
ligandHybridTop__log_> Error: Something went wrong while assigning bonds!
ligandHybridTop__log_> A-> Atom1: 1-N Atom2: 27-H
ligandHybridTop__log_> B-> Atom1: 1-N Atom2: 37-H
ligandHybridTop__log_> Exiting…
"
I am not sure why the error is occuring as openff bond parameters are explicitly stated in the files. It will not allow me to attach the files, but I have uploaded them here: pmx_openff
Hi,
The error likely arises because the atom ordering (indexing) in the itp file (MOL.itp) doesn’t match with the pdb file (mol_gmx.pdb).
Reordering the atoms in pdb file with proper indexing to match the itp will likely resolve the issue.
All the best.