********>mmpbsa.patch

Author: Jason Swails

Date: 4, Oct. 2013

Program: MMPBSA.py

Description: Fix QM/MM-GBSA when there is a net charge in at least one of the
             components

--------------------------------------------------------------------------------

 AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py | 6 ++++--
 AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py       | 4 +++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py
index e9b0554..315fd03 100644
--- AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py
+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py
@@ -122,23 +122,25 @@ def create_inputs(INPUT, prmtop_system, pre):
                   raise CreateInputError('No valid QM residues chosen!')
                com_input['qm_theory'] = "'%s'" % com_input['qm_theory']
                com_input['qmmask'] = "'%s'" % com_input['qmmask']
+               com_input['qmcharge'] = com_input['qmcharge_com']
                gb_mdin = SanderGBInput(com_input)
                gb_mdin.write_input(pre + 'gb_qmmm_com.mdin')
                if not stability:
                   if not rec_input['qmmask']: rec_input['ifqnt'] = 0
                   else: rec_input['qmmask'] = "'%s'" % rec_input['qmmask']
                   rec_input['qm_theory'] = "'%s'" % rec_input['qm_theory']
+                  rec_input['qmcharge'] = rec_input['qmcharge_rec']
                   gb_mdin = SanderGBInput(rec_input)
                   gb_mdin.write_input(pre + 'gb_qmmm_rec.mdin')
                   if not lig_input['qmmask']: lig_input['ifqnt'] = 0
                   else: lig_input['qmmask'] = "'%s'" % lig_input['qmmask']
                   lig_input['qm_theory'] = "'%s'" % lig_input['qm_theory']
+                  lig_input['qmcharge'] = lig_input['qmcharge_lig']
                   gb_mdin = SanderGBInput(lig_input)
                   gb_mdin.write_input(pre + 'gb_qmmm_lig.mdin')
             else:
                gb_mdin = SanderGBInput(INPUT)
-
-         gb_mdin.write_input(pre + 'gb.mdin')
+               gb_mdin.write_input(pre + 'gb.mdin')
 
       if INPUT['pbrun']:
          pb_prog = 'mmpbsa_py_energy'
diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py
index f6d3804..75f82f4 100644
--- AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py
+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py
@@ -46,7 +46,9 @@ def remove(flag, mpi_size=0, fnpre='_MMPBSA_'):
                   fnpre + 'gb_decomp_com.mdin', fnpre + 'gb_decomp_rec.mdin',
                   fnpre + 'gb_decomp_lig.mdin', fnpre + 'pb_decomp_com.mdin',
                   fnpre + 'pb_decomp_rec.mdin', fnpre + 'pb_decomp_lig.mdin',
-                  fnpre + 'ptrajentropy.in', fnpre + 'mutant_ptrajentropy.in']
+                  fnpre + 'ptrajentropy.in', fnpre + 'mutant_ptrajentropy.in',
+                  fnpre + 'gb_qmmm_com.mdin', fnpre + 'gb_qmmm_rec.mdin',
+                  fnpre + 'gb_qmmm_lig.mdin']
 
    # All the extra files we keep for keep_files = 1
    keep_files_1=[fnpre + 'ligand.mdcrd', fnpre + 'ligand.nc',