exclude hydrogens from backbone as well #454

Valdes-Tresanco-MS · Jan 18, 2024 · 99143f7 · 99143f7
1 parent f0da26a
commit 99143f7
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/GMXMMPBSA/createinput.py b/GMXMMPBSA/createinput.py
@@ -201,9 +201,9 @@ def create_inputs(INPUT, prmtop_system, pre):
                  lig_input['gb']['qmmask']) = prmtop_system.Mask(INPUT['gb']['qm_residues'], in_complex=False)
 
                 if INPUT['gb']['exclude_backbone']:
-                    com_input['gb']['qmmask'] = f"({com_input['gb']['qmmask']} & !@N,CA,C,O)"
-                    rec_input['gb']['qmmask'] = f"({rec_input['gb']['qmmask']} & !@N,CA,C,O)"
-                    lig_input['gb']['qmmask'] = f"({lig_input['gb']['qmmask']} & !@N,CA,C,O)"
+                    com_input['gb']['qmmask'] = f"({com_input['gb']['qmmask']} & !@N,CA,HA,C,O)"
+                    rec_input['gb']['qmmask'] = f"({rec_input['gb']['qmmask']} & !@N,CA,HA,C,O)"
+                    lig_input['gb']['qmmask'] = f"({lig_input['gb']['qmmask']} & !@N,CA,HA,C,O)"
 
                 if not com_input['gb']['qmmask']:
                     raise AmberError('No valid QM residues chosen!')