=>> Init data Presuming executables of amber suite to be in /home/programs/amber/amber14/bin =>> Reading input parameters Found VERBOSE => 0 Found PARALLEL => 0 Found PREFIX => snapshot Found PATH => ./ Found START => 1 Found STOP => 31 Found OFFSET => 1 Found COMPLEX => 1 Found RECEPTOR => 1 Found LIGAND => 1 Found COMPT => ./com.prmtop Found RECPT => ./rec.prmtop Found LIGPT => ./lig.prmtop Found GC => 0 Found AS => 0 Found DC => 0 Found MM => 1 Found GB => 1 Found PB => 1 Found MS => 1 Found NM => 0 Found PROC => 2 Found REFE => 0 Found INDI => 1.0 Found EXDI => 80.0 Found SCALE => 2 Found LINIT => 1000 Found ISTRNG => 0.0 Found RADIOPT => 0 Found ARCRES => 0.0625 Found INP => 1 Found SURFTEN => 0.005 Found SURFOFF => 0.00 Found IVCAP => 0 Found CUTCAP => -1.0 Found XCAP => 0.0 Found YCAP => 0.0 Found ZCAP => 0.0 Found DIELC => 1.0 Found IGB => 1 Found GBSA => 1 Found SALTCON => 0.00 Found EXTDIEL => 80.0 Found INTDIEL => 1.0 Found SURFTEN => 0.005 Found SURFOFF => 0.00 Found PROBE => 0.0 =>> Checking sanity Checking GENERAL Checking MM Checking PB Checking GB Checking MS =>> Creating input Sander input PBSA input =>> Calculating energy / entropy contributions Calc contrib for ./snapshot_com.crd.1 Checking atom numbers Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 1 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 2 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 3 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 4 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 5 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Analyzing 6 Ana MM/GB/SAS Ana PBSA Ana MS Calc contrib for ./snapshot_com.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA /home/programs/amber/amber14/bin/sander -O -i pbsa_com.in -o pbsa_com.7.out -c ./snapshot_com.crd.7 -p ./com.prmtop not successful For details see: http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful