
=>> Init data
    Presuming executables of amber suite to be in /home/linda/amber10/exe

=>> Reading input parameters
    Found VERBOSE => 0
    Found PARALLEL => 8
    Found PREFIX => snapshot
    Found PATH => ./snapshot
    Found START => 1
    Found STOP => 50
    Found OFFSET => 1
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./ras-raf.prmtop
    Found RECPT => ./ras.prmtop
    Found LIGPT => ./raf.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 1
    Found MM => 1
    Found GB => 1
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found DCTYPE => 2
    Found COMREC => 1-166
    Found COMLIG => 167-242
    Found COMPRI => 1-166 167-242
    Found RECRES => 1-166
    Found RECPRI => 1-166
    Found RECMAP => 1-166
    Found LIGRES => 1-76
    Found LIGPRI => 1-76
    Found LIGMAP => 167-242
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 2
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0
    Found PROC => 1
    Found MAXCYC => 10000
    Found DRMS => 0.5
    Found IGB => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found SURFTEN => 0.0072
    Found DIELC => 4

=>> Checking sanity
    Checking GENERAL
    Implicit SAS calc by sander
    Checking DC
    Checking MM
    Checking GB

=>> Creating input
    Sander input

=>> Calculating energy / entropy contributions
    Calc contrib for ./snapshot/snapshot_com.crd.1
        Calc MM/GB/SAS
 bad atom type: 2C
        /home/linda/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot/snapshot_com.crd.1 -p ./ras-raf.prmtop not successful
