Dear amber users
I am trying to run for the first time mm_pbsa calculation with amber7
The programs runs until the end but it doesn't calculte the surface area
neither the solvation free energy.
I am studing an organic molecule, and I am using gaff force field.
I got the charges and the radiis for each atom using ptraj with the
option
trajout filename pdb dumpq
Does anyone have an idea why it doesn't calculte everything?
Do I nedd to add some blank line at the end of the files my_delphi.crg
and my_delphi.siz ?
Is there something else I am missing?
Thanks in advance
itzi
Here is my mm_pbsa.log file:
=>> Init data
Presuming executables of amber suite to be in /prod/AMBER/amber7/exe
=>> Reading input parameters
Found PREFIX => tbbnalaS
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 => 1000
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/tbbnalaS_com.crd.1
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_com.crd.2
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_com.crd.3
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_com.crd.4
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_com.crd.5
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_rec.crd.1
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_rec.crd.2
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_rec.crd.3
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_rec.crd.4
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_rec.crd.5
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_lig.crd.1
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_lig.crd.2
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_lig.crd.3
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_lig.crd.4
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
Calc contrib for /home/itziar/TBBNALA/PBSA/tbbnalaS_lig.crd.5
Calc MM/GB/SAS
Generate PDB
Calc PB
Run 0
Generate PQR
Calc MS
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.00542
betaP = 0.092
gammaG = 0.0072
betaG = 0
=>> Reading input
=>> Reordering files
Final order:
1. tbbnalaS_com.all.out: -
2. tbbnalaS_rec.all.out: -
3. tbbnalaS_lig.all.out: -
=>> Reading files
Reading tbbnalaS_com.all.out
Reading tbbnalaS_rec.all.out
Checking CALC
Reading tbbnalaS_lig.all.out
Checking CALC
=>> Treat special parameters
=>> Calc missing parameters
Processing MM GAS
Doing 1 MM ELE
No values for MM_ELE existing -> Skipping
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 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
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 PB PBTOT
Doing 1 PB PBSOL
No values for PB_PBSOL existing -> Skipping
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 PBSOL
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBCAL
Doing 1 PB PBSUR
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
=>> Calc average and stddev
=>> Print output to tbbnalaS_statistics.out
Doing 1 MM DIHED
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Received on Tue Oct 14 2003 - 18:53:00 PDT
