split topology ligand

carlocamilloni · Apr 5, 2022 · 1a7e618 · 1a7e618
1 parent 91d8d31
commit 1a7e618
Show file tree

Hide file tree

Showing 59 changed files with 1,539,273 additions and 1,406,024 deletions.
diff --git a/analysis/new_monomer_analysis.ipynb b/analysis/new_monomer_analysis.ipynb
diff --git a/greta.py b/greta.py
diff --git a/inputs/ABeta/ligandMD_contacts.ndx b/inputs/ABeta/ligandMD_contacts.ndx
diff --git a/inputs/ABeta/ligandMD_contacts_old.ndx b/inputs/ABeta/ligandMD_contacts_old.ndx
diff --git a/inputs/ABeta/topol_ligand.itp b/inputs/ABeta/topol_ligand.itp
diff --git a/multiego.py b/multiego.py
diff --git a/outputs/tests/merge_032/atomtypes.atp b/outputs/tests/merge_032/atomtypes.atp
diff --git a/outputs/tests/merge_032/ffnonbonded.itp b/outputs/tests/merge_032/ffnonbonded.itp
diff --git a/outputs/tests/merge_032/topol_GRETA.top b/outputs/tests/merge_032/topol_GRETA.top
diff --git a/read_input.py b/read_input.py
diff --git a/reference_input/ABeta/fibril.pdb b/reference_input/ABeta/fibril.pdb
diff --git a/reference_input/ABeta/fibril_temp/7q4b.pdb b/reference_input/ABeta/fibril_temp/7q4b.pdb
diff --git a/reference_input/ABeta/fibril_temp/conf.gro b/reference_input/ABeta/fibril_temp/conf.gro
diff --git a/reference_input/ABeta/fibril_temp/fibril.pdb b/reference_input/ABeta/fibril_temp/fibril.pdb
diff --git a/reference_input/ABeta/fibril_temp/multi-ego-basic.ff b/reference_input/ABeta/fibril_temp/multi-ego-basic.ff
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_A.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_A.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_B.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_B.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_C.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_C.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_D.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_D.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_E.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_E.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_F.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_F.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_G.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_G.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_H.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_H.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_I.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_I.itp
diff --git a/reference_input/ABeta/fibril_temp/posre_Protein_chain_R.itp b/reference_input/ABeta/fibril_temp/posre_Protein_chain_R.itp
diff --git a/reference_input/ABeta/fibril_temp/topol.top b/reference_input/ABeta/fibril_temp/topol.top
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_A.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_A.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_B.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_B.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_C.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_C.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_D.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_D.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_E.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_E.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_F.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_F.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_G.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_G.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_H.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_H.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_I.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_I.itp
diff --git a/reference_input/ABeta/fibril_temp/topol_Protein_chain_R.itp b/reference_input/ABeta/fibril_temp/topol_Protein_chain_R.itp
diff --git a/reference_input/ABeta/ligandMD_contacts.ndx b/reference_input/ABeta/ligandMD_contacts.ndx
diff --git a/reference_input/ABeta/multi-ego-basic.ff b/reference_input/ABeta/multi-ego-basic.ff
diff --git a/reference_input/ABeta/native.pdb b/reference_input/ABeta/native.pdb
diff --git a/reference_input/ABeta/native_md.pdb b/reference_input/ABeta/native_md.pdb
diff --git a/reference_input/ABeta/plainMD-noh.gro b/reference_input/ABeta/plainMD-noh.gro
diff --git a/reference_input/ABeta/plainMD_contacts.ndx b/reference_input/ABeta/plainMD_contacts.ndx
diff --git a/reference_input/ABeta/random_coil_contacts.ndx b/reference_input/ABeta/random_coil_contacts.ndx
diff --git a/reference_input/ABeta/temp/g5.gro b/reference_input/ABeta/temp/g5.gro
diff --git a/reference_input/ABeta/temp/g5.pdb b/reference_input/ABeta/temp/g5.pdb
diff --git a/reference_input/ABeta/temp/multi-ego-basic.ff b/reference_input/ABeta/temp/multi-ego-basic.ff
diff --git a/reference_input/ABeta/temp/topol_native_ligand.gro b/reference_input/ABeta/temp/topol_native_ligand.gro
diff --git a/reference_input/ABeta/temp/topol_native_ligand.pdb b/reference_input/ABeta/temp/topol_native_ligand.pdb
diff --git a/reference_input/ABeta/temp/topol_native_ligand_noh.gro b/reference_input/ABeta/temp/topol_native_ligand_noh.gro
diff --git a/reference_input/ABeta/temp/topol_native_ligand_noh.pdb b/reference_input/ABeta/temp/topol_native_ligand_noh.pdb
diff --git a/reference_input/ABeta/topol.top b/reference_input/ABeta/topol.top
diff --git a/reference_input/ABeta/topol_fibril.top b/reference_input/ABeta/topol_fibril.top
diff --git a/reference_input/ABeta/topol_ligand.itp b/reference_input/ABeta/topol_ligand.itp
diff --git a/reference_input/ABeta/topol_ligand.prm b/reference_input/ABeta/topol_ligand.prm
diff --git a/reference_input/ABeta/topol_ligand.top b/reference_input/ABeta/topol_ligand.top
diff --git a/reference_input/ABeta/topol_md.top b/reference_input/ABeta/topol_md.top
diff --git a/reference_input/ABeta/topol_native_ligand.pdb b/reference_input/ABeta/topol_native_ligand.pdb
diff --git a/topology_parser.py b/topology_parser.py
diff --git a/write_output.py b/write_output.py