Dear Amber users
I have two problems regarding mm_pbsa and it`s Binding and Stability
tests. I would be very grateful if someone could help me. One of my
problems has already been posted on Amber List but no one has answered
it (as long as I can see). This is the first problem (regarding
Binding test):
http://archive.ambermd.org/200810/0420.html
I get the same output file when I do this mm_pbsa Bindig test.
And the second problem is my output file for mm_pbsa Stability test:
________________________
=>> Init data
Presuming executables of amber suite to be in /usr/local/amber10/exe
=>> Reading input parameters
Found PREFIX => ras_raf_II_wt
Found PATH => ../01_GenerateSnapshots/
Found COMPLEX => 1
Found RECEPTOR => 0
Found LIGAND => 0
Found COMPT => ../ras_raf_II_wt.prmtop
Found RECPT => XXX
Found LIGPT => XXX
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
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 NPOPT => 1
Found CAVITY_SURFTEN => 0.0072
Found CAVITY_OFFSET => 0.00
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
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
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.2
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.3
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.4
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.5
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.0072
betaP = 0.00
gammaG = 0.0072
betaG = 0.00
=>> Reading input
=>> Reordering files
Final order:
1. ras_raf_II_wt_com.all.out: -
=>> Reading files
Reading ras_raf_II_wt_com.all.out
WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
WARNING: Missing EPB for PB in 1 -> Taken from 0
WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
WARNING: Missing ELRAELE for PB in 2 -> Taken from 1
WARNING: Missing EPB for PB in 2 -> Taken from 1
WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2
WARNING: Missing ELRAELE for PB in 3 -> Taken from 2
WARNING: Missing EPB for PB in 3 -> Taken from 2
WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3
WARNING: Missing ELRAELE for PB in 4 -> Taken from 3
WARNING: Missing EPB for PB in 4 -> Taken from 3
WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4
WARNING: Missing ELRAELE for PB in 5 -> Taken from 4
WARNING: Missing EPB for PB in 5 -> Taken from 4
WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5
WARNING: Missing ELRAELE for PB in 6 -> Taken from 5
WARNING: Missing EPB for PB in 6 -> Taken from 5
WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6
WARNING: Missing ELRAELE for PB in 7 -> Taken from 6
WARNING: Missing EPB for PB in 7 -> Taken from 6
WARNING: Missing PBNONPOL for PB in 8 -> Taken from 7
WARNING: Missing ELRAELE for PB in 8 -> Taken from 7
WARNING: Missing EPB for PB in 8 -> Taken from 7
WARNING: Missing PBNONPOL for PB in 9 -> Taken from 8
WARNING: Missing ELRAELE for PB in 9 -> Taken from 8
WARNING: Missing EPB for PB in 9 -> Taken from 8
WARNING: Missing PBNONPOL for PB in 10 -> Taken from 9
WARNING: Missing ELRAELE for PB in 10 -> Taken from 9
WARNING: Missing EPB for PB in 10 -> Taken from 9
WARNING: Missing PBNONPOL for PB in 11 -> Taken from 10
WARNING: Missing ELRAELE for PB in 11 -> Taken from 10
WARNING: Missing EPB for PB in 11 -> Taken from 10
WARNING: Missing PBNONPOL for PB in 12 -> Taken from 11
WARNING: Missing ELRAELE for PB in 12 -> Taken from 11
WARNING: Missing EPB for PB in 12 -> Taken from 11
WARNING: Missing PBNONPOL for PB in 13 -> Taken from 12
WARNING: Missing ELRAELE for PB in 13 -> Taken from 12
WARNING: Missing EPB for PB in 13 -> Taken from 12
WARNING: Missing PBNONPOL for PB in 14 -> Taken from 13
WARNING: Missing ELRAELE for PB in 14 -> Taken from 13
WARNING: Missing EPB for PB in 14 -> Taken from 13
=>> Treat special parameters
=>> 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
Processing MM ELE
Doing 1 MM ELENB
Doing 1 MM ELE14
Processing MM VDW
Doing 1 MM VDWNB
Doing 1 MM VDW14
Processing GB GBTOT
Doing 1 GB GBSOL
No values for GB_GBSOL existing -> Skipping
Processing GB GBELE
Doing 1 GB GB
Doing 1 MM ELE
Processing GB GBSOL
Doing 1 GB GB
Doing 1 GB GBSUR
Processing PB PBSOL
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBDIS
Processing PB PBELE
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
Processing GB GBTOT
Doing 1 GB GBSOL
Doing 1 MM GAS
Processing PB PBTOT
Doing 1 PB PBSOL
Doing 1 MM GAS
=>> Calc average and stddev
No skew or curtosis when zero variance in moment
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
No skew or curtosis when zero variance in moment
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in addition (+) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
Use of uninitialized value in subtraction (-) at
/usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
=>> Print output to ras_raf_II_wt_statistics.out
=>> Print output (snap) to ras_raf_II_wt_statistics.out.snap
________________________________
I do not know how to solve these problems. Can somebody help me with this?
Are the results (ras_raf_II_wt_statistics.out AND
ras_raf_II_wt_statistics.out.snap) for my mm_pbsa Stability test
representable/correct?
Grateful
Antonija
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Received on Fri Aug 21 2009 - 03:11:24 PDT
