From cd959ce989229e37968fa65f754d4d10183935b3 Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Wed, 1 Dec 2021 12:48:19 +0200 Subject: [PATCH 1/2] fix issue with wrong pkas assigned to terminal residues --- pdb2pqr/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py index 0216e543..d77c6024 100644 --- a/pdb2pqr/main.py +++ b/pdb2pqr/main.py @@ -637,7 +637,7 @@ def non_trivial(args, biomolecule, ligand, definition, is_cif): biomolecule.apply_pka_values( forcefield_.name, args.ph, - {f"{row['res_name']} {row['res_num']} {row['chain_id']}": row["pKa"] for row in pka_df}, + {f"{row['res_name']} {row['res_num']} {row['chain_id']}": row["pKa"] for row in pka_df if row["res_name"] == row["group_type"]}, ) _LOGGER.info("Adding hydrogens to biomolecule.") From bde74be98f9a81c762e6eeda13dbdbb0421336ae Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Wed, 1 Dec 2021 13:10:10 +0200 Subject: [PATCH 2/2] better check. previous caused issues with ASP residues --- pdb2pqr/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py index d77c6024..65b5e042 100644 --- a/pdb2pqr/main.py +++ b/pdb2pqr/main.py @@ -637,7 +637,7 @@ def non_trivial(args, biomolecule, ligand, definition, is_cif): biomolecule.apply_pka_values( forcefield_.name, args.ph, - {f"{row['res_name']} {row['res_num']} {row['chain_id']}": row["pKa"] for row in pka_df if row["res_name"] == row["group_type"]}, + {f"{row['res_name']} {row['res_num']} {row['chain_id']}": row["pKa"] for row in pka_df if row["group_label"].startswith(row["res_name"])}, ) _LOGGER.info("Adding hydrogens to biomolecule.")