********> bugfix.17 
Author: Jason Swails
Date: Fri Sep  2 18:32:30 EDT 2011
Programs: MMPBSA.py
Description: Fix MM/3D-RISM calculations with alanine scanning

cd $AMBERHOME
patch -p0 -N < bugfix.17

-----------------------------------------------------------------------------
--- AmberTools/src/mmpbsa_py/MMPBSA.pypp
+++ AmberTools/src/mmpbsa_py/MMPBSA.pypp
@@ -998,7 +998,7 @@ if not FILES['rewrite_output']: # the next steps need only be executed if we're
          if master: MMPBSA_timer.StartTimer('ptraj')
 
          # create the dummy inpcrd files
-         if isinerr != 1 and (INPUT['gbrun'] or INPUT['pbrun']):
+         if isinerr != 1 and (INPUT['gbrun'] or INPUT['pbrun'] or INPUT['rismrun']):
             os.system('%s %s _MMPBSA_mutant_complexinpcrd.in > _MMPBSA_ptraj9.out 2>&1' % (ptraj, FILES['mutant_complex_prmtop']))
             if not stability and FILES['mutant_receptor_prmtop'] == FILES['receptor_prmtop']:
                os.system('%s %s _MMPBSA_mutant_ligandinpcrd.in > _MMPBSA_ptraj11.out 2>&1' % (ptraj, FILES['mutant_ligand_prmtop']))
-----------------------------------------------------------------------------
workarounds: run GB alanine scanning calculation to create mutant trajectory, 
then run MMPBSA.py with the mutant trajectory (renamed) as the normal trajectory