=>> Init data Presuming executables of amber suite to be in /opt/apps/amber/10/openmpi-mkl/exe =>> Reading input parameters Found PREFIX => snapshot Found PATH => ./ Found COMPLEX => 1 Found RECEPTOR => 1 Found LIGAND => 1 Found COMPT => ../complex.parm7 Found RECPT => ../protein.parm7 Found LIGPT => ../ligand.parm7 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 PRBRAD => 1.4 Found ISTRNG => 0.0 Found RADIOPT => 0 Found NPOPT => 1 Found CAVITY_SURFTEN => 0.0072 Found CAVITY_OFFSET => 0.00 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found DIELC => 1.0 Found IGB => 2 Found GBSA => 1 Found SALTCON => 0.00 Found EXTDIEL => 80.0 Found INTDIEL => 1.0 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found PROBE => 0.0 =>> Checking sanity Checking GENERAL Setting START to default 1 Setting STOP to default 10e10 Setting OFFSET to default 1 Setting VERBOSE to default 0 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 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_com.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.1 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_rec.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.1 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ./snapshot_lig.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS =>> Doing statistics =>> Values of global variables TEMP = 300 R = 8.314 gammaP = 0.0072 betaP = 0.00 gammaG = 0.0072 betaG = 0.00 =>> Reading input =>> Reordering files Final order: 1. snapshot_com.all.out: - 2. snapshot_rec.all.out: - 3. snapshot_lig.all.out: - =>> Reading files Reading snapshot_com.all.out WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1 WARNING: Missing ELRAELE for PB in 0 -> Taken from -1 WARNING: Missing EPB for PB in 0 -> Taken from -1 WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0 WARNING: Missing ELRAELE for PB in 1 -> Taken from 0 WARNING: Missing EPB for PB in 1 -> Taken from 0 WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1 WARNING: Missing ELRAELE for PB in 2 -> Taken from 1 WARNING: Missing EPB for PB in 2 -> Taken from 1 WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2 WARNING: Missing ELRAELE for PB in 3 -> Taken from 2 WARNING: Missing EPB for PB in 3 -> Taken from 2 WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3 WARNING: Missing ELRAELE for PB in 4 -> Taken from 3 WARNING: Missing EPB for PB in 4 -> Taken from 3 WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4 WARNING: Missing ELRAELE for PB in 5 -> Taken from 4 WARNING: Missing EPB for PB in 5 -> Taken from 4 WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5 WARNING: Missing ELRAELE for PB in 6 -> Taken from 5 WARNING: Missing EPB for PB in 6 -> Taken from 5 WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6 WARNING: Missing ELRAELE for PB in 7 -> Taken from 6 WARNING: Missing EPB for PB in 7 -> Taken from 6 WARNING: Missing PBNONPOL for PB in 8 -> Taken from 7 WARNING: Missing ELRAELE for PB in 8 -> Taken from 7 WARNING: Missing EPB for PB in 8 -> Taken from 7 Reading snapshot_rec.all.out Checking CALC WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1 WARNING: Missing ELRAELE for PB in 0 -> Taken from -1 WARNING: Missing EPB for PB in 0 -> Taken from -1 WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0 WARNING: Missing ELRAELE for PB in 1 -> Taken from 0 WARNING: Missing EPB for PB in 1 -> Taken from 0 WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1 WARNING: Missing ELRAELE for PB in 2 -> Taken from 1 WARNING: Missing EPB for PB in 2 -> Taken from 1 WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2 WARNING: Missing ELRAELE for PB in 3 -> Taken from 2 WARNING: Missing EPB for PB in 3 -> Taken from 2 WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3 WARNING: Missing ELRAELE for PB in 4 -> Taken from 3 WARNING: Missing EPB for PB in 4 -> Taken from 3 WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4 WARNING: Missing ELRAELE for PB in 5 -> Taken from 4 WARNING: Missing EPB for PB in 5 -> Taken from 4 WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5 WARNING: Missing ELRAELE for PB in 6 -> Taken from 5 WARNING: Missing EPB for PB in 6 -> Taken from 5 WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6 WARNING: Missing ELRAELE for PB in 7 -> Taken from 6 WARNING: Missing EPB for PB in 7 -> Taken from 6 WARNING: Missing PBNONPOL for PB in 8 -> Taken from 7 WARNING: Missing ELRAELE for PB in 8 -> Taken from 7 WARNING: Missing EPB for PB in 8 -> Taken from 7 Reading snapshot_lig.all.out Checking CALC WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1 WARNING: Missing ELRAELE for PB in 0 -> Taken from -1 WARNING: Missing EPB for PB in 0 -> Taken from -1 WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0 WARNING: Missing ELRAELE for PB in 1 -> Taken from 0 WARNING: Missing EPB for PB in 1 -> Taken from 0 WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1 WARNING: Missing ELRAELE for PB in 2 -> Taken from 1 WARNING: Missing EPB for PB in 2 -> Taken from 1 WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2 WARNING: Missing ELRAELE for PB in 3 -> Taken from 2 WARNING: Missing EPB for PB in 3 -> Taken from 2 WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3 WARNING: Missing ELRAELE for PB in 4 -> Taken from 3 WARNING: Missing EPB for PB in 4 -> Taken from 3 WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4 WARNING: Missing ELRAELE for PB in 5 -> Taken from 4 WARNING: Missing EPB for PB in 5 -> Taken from 4 WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5 WARNING: Missing ELRAELE for PB in 6 -> Taken from 5 WARNING: Missing EPB for PB in 6 -> Taken from 5 WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6 WARNING: Missing ELRAELE for PB in 7 -> Taken from 6 WARNING: Missing EPB for PB in 7 -> Taken from 6 WARNING: Missing PBNONPOL for PB in 8 -> Taken from 7 WARNING: Missing ELRAELE for PB in 8 -> Taken from 7 WARNING: Missing EPB for PB in 8 -> Taken from 7 =>> Treat special parameters =>> Calc missing parameters Processing MM GAS Doing 1 MM ELE No values for MM_ELE existing -> Skipping Processing MM INT Doing 1 MM BOND Doing 1 MM ANGLE Doing 1 MM DIHED Doing 1 MM BOND Doing 1 MM ANGLE Doing 1 MM DIHED Doing 1 MM BOND Doing 1 MM ANGLE Doing 1 MM DIHED Processing MM ELE Doing 1 MM ELENB Doing 1 MM ELE14 Doing 1 MM ELENB Doing 1 MM ELE14 Doing 1 MM ELENB Doing 1 MM ELE14 Processing MM VDW Doing 1 MM VDWNB Doing 1 MM VDW14 Doing 1 MM VDWNB Doing 1 MM VDW14 Doing 1 MM VDWNB Doing 1 MM VDW14 Processing GB GBTOT Doing 1 GB GBSOL No values for GB_GBSOL existing -> Skipping Processing GB GBELE Doing 1 GB GB Doing 1 MM ELE Doing 1 GB GB Doing 1 MM ELE Doing 1 GB GB Doing 1 MM ELE Processing GB GBSOL Doing 1 GB GB Doing 1 GB GBSUR Doing 1 GB GB Doing 1 GB GBSUR Doing 1 GB GB Doing 1 GB GBSUR Processing PB PBSOL Doing 1 PB PBCAL Doing 1 PB PBSUR Doing 1 PB PBDIS Doing 1 PB PBCAL Doing 1 PB PBSUR Doing 1 PB PBDIS Doing 1 PB PBCAL Doing 1 PB PBSUR Doing 1 PB PBDIS Processing PB PBELE Doing 1 PB PBCAL Doing 1 MM ELE Doing 1 PB PBCAL Doing 1 MM ELE Doing 1 PB PBCAL Doing 1 MM ELE Processing PB PBTOT Doing 1 PB PBSOL Doing 1 MM GAS No values for MM_GAS existing -> Skipping Processing MM GAS Doing 1 MM ELE Doing 1 MM VDW Doing 1 MM INT Doing 1 MM ELE Doing 1 MM VDW Doing 1 MM INT Doing 1 MM ELE Doing 1 MM VDW Doing 1 MM INT Processing GB GBTOT Doing 1 GB GBSOL Doing 1 MM GAS Doing 1 GB GBSOL Doing 1 MM GAS Doing 1 GB GBSOL Doing 1 MM GAS Processing PB PBTOT Doing 1 PB PBSOL Doing 1 MM GAS Doing 1 PB PBSOL Doing 1 MM GAS Doing 1 PB PBSOL Doing 1 MM GAS =>> Calc delta from raw data