From 99143f7568f765175e96a1671df7471e566e9ba0 Mon Sep 17 00:00:00 2001 From: Mario E Valdes-Tresanco Date: Thu, 18 Jan 2024 01:50:43 -0700 Subject: [PATCH] exclude hydrogens from backbone as well #454 --- GMXMMPBSA/createinput.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/GMXMMPBSA/createinput.py b/GMXMMPBSA/createinput.py index ca25e3b9..dc6791a7 100644 --- 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!')