=>> Init data
    Presuming executables of amber suite to be in /home/braf/md/amber11/bin

=>> Reading input parameters
    Found VERBOSE => 0
    Found PARALLEL => 0
    Found PREFIX => snapshot
    Found PATH => ./
    Found START => 1
    Found STOP => 250
    Found OFFSET => 1
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./com.top
    Found RECPT => ./rec.top
    Found LIGPT => ./cel.top
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 1
    Found MS => 1
    Found NM => 1
    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 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 => 2
    Found GBSA => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.005
    Found SURFOFF => 0.00
    Found IGB => 1
    Found DIELC => 1
    Found PROC => 1
    Found MAXCYC => 10000
    Found DRMS => 0.5
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found SURFTEN => 0.0072
    Found PROBE => 0.0

=>> Checking sanity
    Checking GENERAL
    Checking MM
    Checking NM
    Checking PB
    Checking GB
    Checking MS

=>> Creating input
    Sander input
    PBSA input
    NABnmode input

=>> Calculating energy / entropy contributions
    Calc contrib for ./snapshot_com.crd.1
        Checking atom numbers
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Minimize structure and calc entropy