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CHARMM and AMBER forcefields for OpenMM (with small molecule support)
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How can I convert charmm interface FF to openmm xml? #251

Open wangm23456 opened 1 year ago

wangm23456 commented 1 year ago

charmm interface FF from charmm-gui

the rtf like this:

  • INTERFACE FF
  • topology for nanomaterials

  • 36 1

the prm title:

  • INTERFACE FF
  • topology and parameter for caly minerals, cement minerals

the str file for simulation:

  • GENERATED BY CHARMM-GUI
  • Stream file for topology and parameter reading

! protein topology and parameter open read card unit 10 name toppar/top_all36_prot.rtf read rtf card unit 10

open read card unit 20 name toppar/par_all36m_prot.prm read para card unit 20 flex

! nucleic acids open read card unit 10 name toppar/top_all36_na.rtf read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_na.prm read para card unit 20 append flex

! carbohydrates open read card unit 10 name toppar/top_all36_carb.rtf read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_carb.prm read para card unit 20 append flex

! lipids open read card unit 10 name toppar/top_all36_lipid.rtf read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_lipid.prm read para card unit 20 append flex

! CGENFF open read card unit 10 name toppar/top_all36_cgenff.rtf read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_cgenff.prm read para card unit 20 append flex

! Phosphates and Sulfates stream toppar/toppar_all36_moreions.str

! Interface FF open read card unit 10 name toppar/top_interface.rtf read rtf card unit 10 append

open read card unit 10 name toppar/par_interface.prm read para card unit 10 append flex

stream toppar/toppar_all36_nano_lig.str stream toppar/toppar_all36_nano_lig_patch.str

! Additional topologies and parameters for synthetic polymer stream toppar/toppar_all36_synthetic_polymer.str stream toppar/toppar_all36_synthetic_polymer_patch.str stream toppar/toppar_all36_polymer_solvent.str

! Additional topologies and parameters for water and ions stream toppar/toppar_water_ions.str stream toppar/toppar_dum_noble_gases.str stream toppar/toppar_ions_won.str stream toppar/cam.str

! Additional topologies and parameters for protein stream toppar/toppar_all36_prot_arg0.str stream toppar/toppar_all36_prot_c36m_d_aminoacids.str stream toppar/toppar_all36_prot_fluoro_alkanes.str stream toppar/toppar_all36_prot_heme.str stream toppar/toppar_all36_prot_na_combined.str stream toppar/toppar_all36_prot_retinol.str stream toppar/toppar_all36_prot_model.str stream toppar/toppar_all36_prot_modify_res.str

! Additional topologies and parameters for nucleic acids stream toppar/toppar_all36_na_nad_ppi.str stream toppar/toppar_all36_na_rna_modified.str

! Additional topologies and parameters for lipids stream toppar/toppar_all36_lipid_sphingo.str stream toppar/toppar_all36_lipid_archaeal.str stream toppar/toppar_all36_lipid_bacterial.str stream toppar/toppar_all36_lipid_cardiolipin.str stream toppar/toppar_all36_lipid_cholesterol.str stream toppar/toppar_all36_lipid_dag.str stream toppar/toppar_all36_lipid_inositol.str stream toppar/toppar_all36_lipid_lnp.str stream toppar/toppar_all36_lipid_lps.str stream toppar/toppar_all36_lipid_mycobacterial.str stream toppar/toppar_all36_lipid_miscellaneous.str stream toppar/toppar_all36_lipid_model.str stream toppar/toppar_all36_lipid_prot.str stream toppar/toppar_all36_lipid_tag.str stream toppar/toppar_all36_lipid_yeast.str stream toppar/toppar_all36_lipid_hmmm.str stream toppar/toppar_all36_lipid_detergent.str stream toppar/toppar_all36_lipid_ether.str

! Additional topologies and parameters for carbohydrates stream toppar/toppar_all36_carb_glycolipid.str stream toppar/toppar_all36_carb_glycopeptide.str stream toppar/toppar_all36_carb_imlab.str

! Additional topologies and parameters for spin/fluorophore labels stream toppar/toppar_all36_label_spin.str stream toppar/toppar_all36_label_fluorophore.str

wangm23456 commented 1 year ago

the input yaml:

- sourcePackage: charmm36
  sourcePackageVersion: lnk.tgz
- Destination: charmm36_lnk.xml
  Source:
    include:
     - lnk/top_interface.rtf
     - lnk/par_interface.prm

File "/data/home/wangmeng/magic/openmm/FF/CHARMM/convert.py", line 128, in convert_yaml params_omm.write(ffxml_filename, provenance=provenance, charmm_imp=True, separate_ljforce=True) File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/openmm/parameters.py", line 65, in wrapper return func(*args, **kwargs) File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/openmm/parameters.py", line 392, in write [valid_residues_for_patch, valid_patches_for_residue] = self._determine_valid_patch_combinations(skip_residues) File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/openmm/parameters.py", line 715, in _determine_valid_patch_combinations residue_compatibilities = [ residue.patch_is_compatible(patch) for residue in residues ] File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/openmm/parameters.py", line 715, in residue_compatibilities = [ residue.patch_is_compatible(patch) for residue in residues ] File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/modeller/residue.py", line 538, in patch_is_compatible self.apply_patch(patch) File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/parmed/modeller/residue.py", line 511, in apply_patch if not nx.is_connected(G): File "<class 'networkx.utils.decorators.argmap'> compilation 4", line 4, in argmap_is_connected_1 File "/data/home/wangmeng/.pyenv/versions/miniconda3-latest/envs/openmm/lib/python3.10/site-packages/networkx/algorithms/components/connected.py", line 142, in is_connected raise nx.NetworkXPointlessConcept( networkx.exception.NetworkXPointlessConcept: ('Connectivity is undefined ', 'for the null graph.')