[AMBER] mm_pbsa-Binding and Stability tests?

From: Antonija Tomić <Antonija.Tomic.irb.hr>
Date: Fri, 21 Aug 2009 11:04:35 +0100

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
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