AMBER: MM-PBSA error in Amber10: possible bug?

From: Pablo Englebienne <pablo.englebienne.mcgill.ca>
Date: Fri, 31 Oct 2008 23:38:15 -0400

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
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