=>> Init data Presuming executables of amber suite to be in /usr/local/AMBER/amber10/exe =>> Reading input parameters Found PREFIX => DENGUE_NpH Found PATH => ../01_GenerateSnapshots/ Found COMPLEX => 1 Found RECEPTOR => 1 Found LIGAND => 1 Found COMPT => ../DENGUE_DIM_COM.top Found RECPT => ../DENGUE_MONO.top Found LIGPT => ../DENGUE_MONO.top 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 => 5 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 ../01_GenerateSnapshots/DENGUE_NpH_com.crd.1 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.10 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.11 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_com.crd.12 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.1 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.10 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.11 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_rec.crd.12 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.1 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.2 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.3 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.4 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.5 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.6 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.7 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.8 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.9 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.10 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.11 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS Calc contrib for ../01_GenerateSnapshots/DENGUE_NpH_lig.crd.12 Calc MM/GB/SAS Generate PDB Center PDB Calc PBSA Generate PQR Calc MS =>> Doing statistics =>> Reading input =>> Reordering files Final order: 1. DENGUE_NpH_com.all.out: - 2. DENGUE_NpH_rec.all.out: - 3. DENGUE_NpH_lig.all.out: - =>> Reading files Reading DENGUE_NpH_com.all.out WARNING: Missing PBCAV for PB in 0 -> Taken from -1 WARNING: Missing PBDIS for PB in 0 -> Taken from -1 WARNING: Missing SURF for MS in 0 -> Taken from -1 WARNING: Missing PBCAV for PB in 1 -> Taken from 0 WARNING: Missing PBDIS for PB in 1 -> Taken from 0 WARNING: Missing SURF for MS in 1 -> Taken from 0 WARNING: Missing PBCAV for PB in 2 -> Taken from 1 WARNING: Missing PBDIS for PB in 2 -> Taken from 1 WARNING: Missing SURF for MS in 2 -> Taken from 1 WARNING: Missing PBCAV for PB in 3 -> Taken from 2 WARNING: Missing PBDIS for PB in 3 -> Taken from 2 WARNING: Missing SURF for MS in 3 -> Taken from 2 WARNING: Missing PBCAV for PB in 4 -> Taken from 3 WARNING: Missing PBDIS for PB in 4 -> Taken from 3 WARNING: Missing SURF for MS in 4 -> Taken from 3 WARNING: Missing BOND for MM in 5 -> Taken from 4 WARNING: Missing ELE14 for MM in 5 -> Taken from 4 WARNING: Missing ELENB for MM in 5 -> Taken from 4 WARNING: Missing VDWNB for MM in 5 -> Taken from 4 WARNING: Missing DIHED for MM in 5 -> Taken from 4 WARNING: Missing ANGLE for MM in 5 -> Taken from 4 WARNING: Missing VDW14 for MM in 5 -> Taken from 4 WARNING: Missing GB for GB in 5 -> Taken from 4 WARNING: Missing PB for PB in 5 -> Taken from 4 WARNING: Missing PBCAV for PB in 5 -> Taken from 4 WARNING: Missing PBDIS for PB in 5 -> Taken from 4 WARNING: Missing SURF for MS in 5 -> Taken from 4 WARNING: Missing PBCAV for PB in 6 -> Taken from 5 WARNING: Missing PBDIS for PB in 6 -> Taken from 5 WARNING: Missing SURF for MS in 6 -> Taken from 5 WARNING: Missing PBCAV for PB in 7 -> Taken from 6 WARNING: Missing PBDIS for PB in 7 -> Taken from 6 WARNING: Missing SURF for MS in 7 -> Taken from 6 WARNING: Missing PBCAV for PB in 8 -> Taken from 7 WARNING: Missing PBDIS for PB in 8 -> Taken from 7 WARNING: Missing SURF for MS in 8 -> Taken from 7 WARNING: Missing PBCAV for PB in 9 -> Taken from 8 WARNING: Missing PBDIS for PB in 9 -> Taken from 8 WARNING: Missing SURF for MS in 9 -> Taken from 8 WARNING: Missing PBCAV for PB in 10 -> Taken from 9 WARNING: Missing PBDIS for PB in 10 -> Taken from 9 WARNING: Missing SURF for MS in 10 -> Taken from 9 WARNING: Missing PBCAV for PB in 11 -> Taken from 10 WARNING: Missing PBDIS for PB in 11 -> Taken from 10 WARNING: Missing SURF for MS in 11 -> Taken from 10 WARNING: Missing PBCAV for PB in 12 -> Taken from 11 WARNING: Missing PBDIS for PB in 12 -> Taken from 11 WARNING: Missing SURF for MS in 12 -> Taken from 11 WARNING: Missing PBCAV for PB in 13 -> Taken from 12 WARNING: Missing PBDIS for PB in 13 -> Taken from 12 WARNING: Missing SURF for MS in 13 -> Taken from 12 WARNING: Missing PBCAV for PB in 14 -> Taken from 13 WARNING: Missing PBDIS for PB in 14 -> Taken from 13 WARNING: Missing SURF for MS in 14 -> Taken from 13 WARNING: Missing PBCAV for PB in 15 -> Taken from 14 WARNING: Missing PBDIS for PB in 15 -> Taken from 14 WARNING: Missing SURF for MS in 15 -> Taken from 14 WARNING: Missing PBCAV for PB in 16 -> Taken from 15 WARNING: Missing PBDIS for PB in 16 -> Taken from 15 WARNING: Missing SURF for MS in 16 -> Taken from 15 WARNING: Missing PB for PB in 17 -> Taken from 16 WARNING: Missing PBCAV for PB in 17 -> Taken from 16 WARNING: Missing PBDIS for PB in 17 -> Taken from 16 WARNING: Missing SURF for MS in 17 -> Taken from 16 WARNING: Missing PBCAV for PB in 18 -> Taken from 17 WARNING: Missing PBDIS for PB in 18 -> Taken from 17 WARNING: Missing SURF for MS in 18 -> Taken from 17 WARNING: Missing PBCAV for PB in 19 -> Taken from 18 WARNING: Missing PBDIS for PB in 19 -> Taken from 18 WARNING: Missing SURF for MS in 19 -> Taken from 18 WARNING: Missing PBCAV for PB in 20 -> Taken from 19 WARNING: Missing PBDIS for PB in 20 -> Taken from 19 WARNING: Missing SURF for MS in 20 -> Taken from 19 WARNING: Missing PBCAV for PB in 21 -> Taken from 20 WARNING: Missing PBDIS for PB in 21 -> Taken from 20 WARNING: Missing SURF for MS in 21 -> Taken from 20 WARNING: Missing PBCAV for PB in 22 -> Taken from 21 WARNING: Missing PBDIS for PB in 22 -> Taken from 21 WARNING: Missing SURF for MS in 22 -> Taken from 21 WARNING: Missing PBCAV for PB in 23 -> Taken from 22 WARNING: Missing PBDIS for PB in 23 -> Taken from 22 WARNING: Missing SURF for MS in 23 -> Taken from 22 WARNING: Missing PBCAV for PB in 24 -> Taken from 23 WARNING: Missing PBDIS for PB in 24 -> Taken from 23 WARNING: Missing SURF for MS in 24 -> Taken from 23 WARNING: Missing PBCAV for PB in 25 -> Taken from 24 WARNING: Missing PBDIS for PB in 25 -> Taken from 24 WARNING: Missing SURF for MS in 25 -> Taken from 24 WARNING: Missing PBCAV for PB in 26 -> Taken from 25 WARNING: Missing PBDIS for PB in 26 -> Taken from 25 WARNING: Missing SURF for MS in 26 -> Taken from 25 WARNING: Missing PBCAV for PB in 27 -> Taken from 26 WARNING: Missing PBDIS for PB in 27 -> Taken from 26 WARNING: Missing SURF for MS in 27 -> Taken from 26 WARNING: Missing BOND for MM in 28 -> Taken from 27 WARNING: Missing ELE14 for MM in 28 -> Taken from 27 WARNING: Missing ELENB for MM in 28 -> Taken from 27 WARNING: Missing VDWNB for MM in 28 -> Taken from 27 WARNING: Missing DIHED for MM in 28 -> Taken from 27 WARNING: Missing ANGLE for MM in 28 -> Taken from 27 WARNING: Missing VDW14 for MM in 28 -> Taken from 27 WARNING: Missing GB for GB in 28 -> Taken from 27 WARNING: Missing PB for PB in 28 -> Taken from 27 WARNING: Missing PBCAV for PB in 28 -> Taken from 27 WARNING: Missing PBDIS for PB in 28 -> Taken from 27 WARNING: Missing SURF for MS in 28 -> Taken from 27 Reading DENGUE_NpH_rec.all.out Checking consistency of CALC Checking consistency of DATA Reading DENGUE_NpH_lig.all.out Checking consistency of CALC Checking consistency of DATA =>> Values of parameters TEMP = 300 R = 8.314 gammaP = 0.0072 betaP = 0.00 gammaG = 0.0072 betaG = 0.00 =>> 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