Hi, I'm trying to run some MM-PBSA calculations on Amber10 (patched up
to bugfix 8; bugfix.9 and bugfix.10 apparently do not affect this
issue so it's essentially fully patched), and I'm running into
trouble. This same problem has been recently reported by other users,
but I still didn't see a solution posted on the list:
-
http://archive.ambermd.org/200810/0006.html
-
http://archive.ambermd.org/200810/0050.html
-
http://archive.ambermd.org/200810/0283.html
I found that the same problem I see with my system (and what the other
users were seeing) happens when I try to run the test on $AMBERHOME/
src/mm_pbsa:
$ cd $AMBERHOME/src/mm_pbsa/Examples
$ make test.all
cd 01_GenerateSnapshots; /opt/amber/amber10/exe/mm_pbsa.pl mm_pbsa.in
> mm_pbsa.log 2>&1
cd 02_MMPBSA_Stability; /opt/amber/amber10/exe/mm_pbsa.pl mm_pbsa.in >
mm_pbsa.log 2>&1
cd 03_MMPBSA_Binding; /opt/amber/amber10/exe/mm_pbsa.pl mm_pbsa.in >
mm_pbsa.log 2>&1
make: *** [test.MMPBSA_Binding] Error 26
This is the content of 03_MMPBSA_Binding/mm_pbsa.log:
--[mm_pbsa.log]--
=>> Init data
Presuming executables of amber suite to be in /opt/amber/amber10/
exe
=>> Reading input parameters
Found PREFIX => ras_raf_II_wt
Found PATH => ../01_GenerateSnapshots/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ../ras_raf_II_wt.prmtop
Found RECPT => ../ras_II_wt.prmtop
Found LIGPT => ../raf_wt.prmtop
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
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_rec.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_rec.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_rec.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_rec.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_rec.crd.5
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.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_lig.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_lig.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_lig.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_lig.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: -
2. ras_raf_II_wt_rec.all.out: -
3. ras_raf_II_wt_lig.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
Reading ras_raf_II_wt_rec.all.out
Checking CALC
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
Reading ras_raf_II_wt_lig.all.out
Checking CALC
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
=>> 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
Doing 1 MM BOND
Doing 1 MM ANGLE
Doing 1 MM DIHED
Doing 1 MM BOND
Doing 1 MM ANGLE
Doing 1 MM DIHED
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 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 GB GBTOT
Doing 1 GB GBSOL
No values for GB_GBSOL existing -> Skipping
Processing GB GBELE
Doing 1 GB GB
Doing 1 MM ELE
Doing 1 GB GB
Doing 1 MM ELE
Doing 1 GB GB
Doing 1 MM ELE
Processing GB GBSOL
Doing 1 GB GB
Doing 1 GB GBSUR
Doing 1 GB GB
Doing 1 GB GBSUR
Doing 1 GB GB
Doing 1 GB GBSUR
Processing PB PBSOL
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBDIS
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBDIS
Doing 1 PB PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBDIS
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 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
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 GB GBTOT
Doing 1 GB GBSOL
Doing 1 MM GAS
Doing 1 GB GBSOL
Doing 1 MM GAS
Doing 1 GB GBSOL
Doing 1 MM GAS
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 from raw data
No data for 0+0 PB ELRAELE 0
--[mm_pbsa.log]--
It looks like there is some missing data, or data that is not properly
being processed by the script.
I did some quick insight, and it seems to me that the following line
in mm_pbsa_calceneent.pm:
--[mm_pbsa_calceneent.pm]--
print OUT "ELRAELE = ", 0.5 * ${lraele} * $kcal2kt, "\n";
--[mm_pbsa_calceneent.pm]--
should print a line starting with ELRAELE in the *_all.out files, but
there is no ELRAELE in any of the *_all.out.save files. Even a little
bit before that line in mm_pbsa_calceneent.pm, the section that
defined the value for $lraele looks for a line with 'Protein-solvent
interactions' in it in the PBSA output file, but no line contains that
text in the output file:
--[mm_pbsa_calceneent.pm]--
while(defined($line = <IN>)){
if($r_gen->{"DC"}){
if($line =~ /^TDC/ || $line =~ /^SDC/ || $line =~ /^BDC/){
print OUT "PB_" . $line;
}
}
elsif($line =~ /FINAL RESULTS/){
$finalflg = 1;
}
elsif($line =~ /Protein-solvent interactions: +(-?\d+\.\d+) +(-?\d
+\.\d+)/){ <-- this line
$lraele = $1;
$lravdw = $2;
}
--[mm_pbsa_calceneent.pm]--
It looks like perhaps the output of the PBSA calculation changed in
the last version, and the mm_pbsa.pl is not picking the results up
correctly?
Regards,
--
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501 Fax (514) 398-2382
"Progress is made by lazy men looking for easier ways to do things." -
Robert A. Heinlein
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Received on Sun Nov 02 2008 - 05:09:41 PST
