AMBER Archive (2009)

Subject: Re: [AMBER] mm_pbsa-Binding and Stability tests?

From: Ray Luo (ray.luo_at_uci.edu)
Date: Fri Aug 21 2009 - 16:29:58 CDT

Antonijia,

Please first patch the latest bug fixes for Amber10 and see whether you
still have the following error messages.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Antonija Tomić wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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