
=>> Init data
    Presuming executables of amber suite to be in /home/rok/SandBox-091207/amber9/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./Snapshots/
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./Prmtop/ras-raf.prmtop
    Found RECPT => ./Prmtop/ras.prmtop
    Found LIGPT => ./Prmtop/raf.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 0
    Found PB => 1
    Found MS => 0
    Found NM => 0
    Found PROC => 3
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2
    Found LINIT => 1000
    Found PRBRAD => 1.4
    Found RADIOPT => 0
    Found SRAD => 1.4
    Found BCFL => 2
    Found SRFM => 1
    Found CHGM => 1
    Found SWIN => 0.3
    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
    Checking MM
    Checking PB

=>> Creating input
    Sander input
    iAPBS input

=>> Calculating energy / entropy contributions
    Calc contrib for ./Snapshots/snapshot_com.crd.1
        Calc MM/GB/SAS
        Calc Amber/iAPBS
    Calc contrib for ./Snapshots/snapshot_com.crd.2
        Calc MM/GB/SAS
        Calc Amber/iAPBS
    Calc contrib for ./Snapshots/snapshot_rec.crd.1
        Calc MM/GB/SAS
        Calc Amber/iAPBS
    Calc contrib for ./Snapshots/snapshot_rec.crd.2
        Calc MM/GB/SAS
        Calc Amber/iAPBS
    Calc contrib for ./Snapshots/snapshot_lig.crd.1
        Calc MM/GB/SAS
        Calc Amber/iAPBS
    Calc contrib for ./Snapshots/snapshot_lig.crd.2
        Calc MM/GB/SAS
        Calc Amber/iAPBS

=>> Doing statistics
=>> Values of global variables
    TEMP   = 300
    R      = 8.314
    gammaP = 1
    betaP  = 0
    gammaG = 0.0072
    betaG  = 0
=>> 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 PBCAV for PB in 0 -> Taken from -1
    WARNING: Missing PBDIS for PB 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
    Reading snapshot_rec.all.out
    Checking CALC
    WARNING: Missing PBCAV for PB in 0 -> Taken from -1
    WARNING: Missing PBDIS for PB 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
    Reading snapshot_lig.all.out
    Checking CALC
    WARNING: Missing PBCAV for PB in 0 -> Taken from -1
    WARNING: Missing PBDIS for PB 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
=>> Treat special parameters
rok INSIDE
rok INSIDE
rok INSIDE
rok INSIDE
rok INSIDE
rok INSIDE
=>> 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 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 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
=>> Calc average and stddev
=>> Print output to snapshot_statistics.out
