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Dear amber users,
I am trying to perform a mm_pbsa calculation but all the time I get the following mesage :
tmp.pdb not opened
Could someone tell me which one is the problem? any suggestion to solve it?
Thank you in advance
Itziar
Here is my log file:
=>> Init data
Presuming executables of amber suite to be in /prod/AMBER/amber7/exe
=>> Reading input parameters
Found PREFIX => pbsa
Found PATH => /home/itziar/TBBNALA/PBSA/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => tbbnala.top
Found RECPT => nala.top
Found LIGPT => tbb.top
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 0
Found PB => 1
Found MS => 1
Found NM => 0
Found FOCUS => 0
Found INDI => 1.0
Found EXDI => 80.0
Found PERFIL => 80.0
Found SCALE => 2
Found LINIT => 1000
Found BNDCON => 4
Found CHARGE => ./my_delphi.crg
Found SIZE => ./my_delphi.siz
Found SURFTEN => 0.00542
Found SURFOFF => 0.092
Found PROBE => 1.4
Found RADII => ./atmtypenumbers
Found BOX => NO
Found NTOTAL => 133
Found NSTART => 40
Found NSTOP => 5040
Found NFREQ => 25
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 1
Found LSTOP => 116
Found NUMBER_REC_GROUPS => 1
Found RSTART => 117
Found RSTOP => 133
Found TRAJECTORY => ./tbbnalaS_md.trj
Found DELPHI => /prod/AMBER/delphi/delphi
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
Checking MM
Checking DELPHI
Checking MS
=>> Creating input
Sander input
Delphi input
make_crd input
=>> Creating coordinates
Executing makecrd
=>> Calculating energy / entropy contributions
Calc contrib for /home/itziar/TBBNALA/PBSA/pbsa_com.crd.1
Calc MM/GB/SAS
Generate PDB
history='fc -l'
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Received on Mon Oct 13 2003 - 11:53:01 PDT
