AMBER Archive (2009)

Subject: [AMBER] Error in MM PBSA

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Thu Jun 04 2009 - 09:58:43 CDT

Dear All
am doing the the binding free energy calculation for another ligand...

when i run :
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
i get the following error:

/opt/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c
/home/bharatam/amberresults_w/amberresults_ligand/snapshot_com.crd.1 -p
/home/bharatam/amberresults_w/amb31/prot_lig.prmtop not successful

how can i fix this one?

I am pasting the
1. extract_coords.mmpbsa
2 extract_coords.log
3. binding_energy.mmpbsa
4. binding_energy.log

thank you

1. extract_coords.mmpbsa:

PREFIX snapshot
PATH /home/bharatam/amberresults_w/amberresults31
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT /home/bharatam/amberresults_w/amb31/A31.prmtop
RECPT /home/bharatam/amberresults_w/amb31/A.prmtop
LIGPT /home/bharatam/amberresults_w/amb31/31.prmtop
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
#
################################################################################
@MAKECRD

#
BOX YES
NTOTAL 32127
NSTART 1
NSTOP 100
NFREQ 1
#
NUMBER_LIG_GROUPS 1
LSTART 3734
LSTOP 3777
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3715
#
#################################################################################
@TRAJECTORY

TRAJECTORY /home/bharatam/amberresults_q/amb31/prod1.mdcrd
TRAJECTORY /home/bharatam/amberresults_q/amb31/prod2.mdcrd
#
################################################################################
@PROGRAMS
#
# Additional program executables can be defined here
#
#

2. extract_coords.log

=>> Init
data
    Presuming executables of amber suite
to be in /opt/amber10/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH =>
/home/bharatam/amberresults_w/amberresults31
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT =>
/home/bharatam/amberresults_w/amb31/A31.prmtop
    Found RECPT =>
/home/bharatam/amberresults_w/amb31/A.prmtop
    Found LIGPT =>
/home/bharatam/amberresults_w/amb31/31.prmtop
    Found GC => 1
    Found AS => 0
    Found DC => 0
    Found MM => 0
    Found GB => 0
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found BOX => YES
    Found NTOTAL => 32127
    Found NSTART => 1
    Found NSTOP => 100
    Found NFREQ => 1
    Found NUMBER_LIG_GROUPS => 1
    Found LSTART => 3734
    Found LSTOP => 3777
    Found NUMBER_REC_GROUPS => 1
    Found RSTART => 1
    Found RSTOP => 3715
    Found TRAJECTORY =>
/home/bharatam/amberresults_q/amb31/prod1.mdcrd
    Found TRAJECTORY =>
/home/bharatam/amberresults_q/amb31/prod2.mdcrd

=>> 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 GC
    Checking TRAJ

=>> Creating input
    make_crd input

=>> Creating coordinates
    Executing makecrd
  
Amber8 Module: make_crg_hg
  
usage: make_crd_hg < trajectory_file
  
Box info found: 52.8430000000000 22.7740000000000
   18.8610000000000
Box info found: 16.9110000000000 54.1130000000000
   36.6450000000000
Box info found: 28.4270000000000 27.5410000000000
   39.0590000000000
Box info found: 52.1410000000000 11.8680000000000
   25.2730000000000
Box info found: 46.7290000000000 93.8590000000000
   24.9600000000000
Box info found: 26.5330000000000 66.3580000000000
   93.8740000000000
Box info found: 38.0380000000000 18.2330000000000
   54.9480000000000
Box info found: 34.2650000000000 44.1740000000000
   55.4780000000000
Box info found: 16.9190000000000 30.0590000000000
   20.9830000000000
Box info found: -2.95200000000000 38.6430000000000
   58.7070000000000
Box info found: 67.1480000000000 40.6250000000000
   22.1560000000000
Box info found: 41.8250000000000 25.3730000000000
   95.5360000000000
Box info found: 69.2710000000000 25.9010000000000
   30.7570000000000
Box info found: 7.63500000000000 10.8460000000000
   51.3660000000000
Box info found: -4.74900000000000 37.0050000000000
   99.4760000000000
Box info found: 24.1140000000000 35.0380000000000
   15.6580000000000
Box info found: 35.6160000000000 16.6070000000000
   68.5440000000000
Box info found: 24.2830000000000 61.0090000000000
   3.55100000000000
Box info found: 1.29400000000000 48.4400000000000
   64.4490000000000
Box info found: 41.1540000000000 14.3250000000000
  -17.9530000000000
Box info found: 21.9260000000000 42.5770000000000
   64.6110000000000
Box info found: 111.419000000000 -1.41100000000000
   54.4480000000000
Box info found: 25.1640000000000 72.3140000000000
   18.0940000000000
Box info found: 31.3080000000000 12.5270000000000
   95.3370000000000
Box info found: 22.2560000000000 2.04500000000000
  -8.89800000000000
Box info found: 24.5330000000000 -25.7080000000000
   57.5490000000000
Box info found: 11.4940000000000 42.8770000000000
   34.8270000000000
Box info found: -0.669000000000000 47.2240000000000
   8.42100000000000
Box info found: 15.7650000000000 0.740000000000000
   38.2690000000000
Box info found: 28.8180000000000 5.09100000000000
   65.4730000000000
Box info found: 59.3860000000000 43.6810000000000
  -3.12900000000000
Box info found: 53.1920000000000 79.9940000000000
   98.9040000000000
Box info found: 32.7610000000000 14.9630000000000
   29.2980000000000
Box info found: -15.4480000000000 57.1130000000000
   12.9900000000000
Box info found: -20.5660000000000 35.6160000000000
  -11.8260000000000
Box info found: -5.60400000000000 -12.0920000000000
  -6.37000000000000
Box info found: 24.9500000000000 52.7220000000000
   67.8710000000000
Box info found: 18.0210000000000 32.3590000000000
   29.0930000000000
Box info found: 10.9160000000000 39.3610000000000
   47.1680000000000
Box info found: 16.7160000000000 38.2340000000000
   50.8060000000000
Box info found: 100.905000000000 78.0400000000000
   60.3420000000000
Box info found: 52.2990000000000 58.8350000000000
  -2.62800000000000
Box info found: 27.0950000000000 47.3420000000000
   51.9590000000000
Box info found: 5.79800000000000 40.0280000000000
   26.8480000000000
Box info found: 62.5700000000000 9.27300000000000
   9.47500000000000
Box info found: 53.6680000000000 36.0780000000000
   9.15500000000000
Box info found: 55.1120000000000 0.282000000000000
   16.3980000000000
Box info found: 46.9120000000000 32.0200000000000
  -33.8290000000000
        Skipped title_line
Box info found: 43.5340000000000 -7.87300000000000
   69.0840000000000
Box info found: 54.7510000000000 21.5270000000000
   59.9250000000000
Box info found: 98.4870000000000 39.1740000000000
   57.7180000000000
Box info found: 71.7410000000000 25.0680000000000
   28.2510000000000
Box info found: 46.1570000000000 -21.6730000000000
   2.39000000000000
Box info found: 29.1180000000000 26.3760000000000
   20.4110000000000
Box info found: 6.38900000000000 34.8170000000000
   6.13400000000000
Box info found: -3.15800000000000 43.0750000000000
   18.9190000000000
Box info found: 87.0770000000000 8.22900000000000
  -19.4580000000000
Box info found: 34.2650000000000 -3.74200000000000
   85.5290000000000
Box info found: 50.9110000000000 50.0090000000000
  -5.95200000000000
Box info found: 22.0960000000000 75.1990000000000
   48.7670000000000
Box info found: 91.6900000000000 30.1340000000000
   16.0670000000000
Box info found: 30.9670000000000 72.4630000000000
  -30.1200000000000
Box info found: -1.24000000000000 0.818000000000000
   80.4510000000000
Box info found: 51.2970000000000 -12.0470000000000
  -10.0840000000000
Box info found: 38.8850000000000 16.4310000000000
  -18.4610000000000
Box info found: -22.7560000000000 58.7590000000000
   65.4910000000000
Box info found: 63.0760000000000 30.9020000000000
   64.5880000000000
Box info found: 82.6680000000000 31.5900000000000
   7.15400000000000
Box info found: 6.32100000000000 45.3070000000000
   151.343000000000
Box info found: 30.5890000000000 16.3580000000000
   15.9540000000000
Box info found: 16.1340000000000 7.80600000000000
  -2.74700000000000
Box info found: 76.5080000000000 -17.2160000000000
   64.2020000000000
Box info found: 13.0740000000000 -55.7100000000000
   42.6410000000000
Box info found: 23.2840000000000 23.0810000000000
   53.6940000000000
Box info found: 48.5340000000000 38.3920000000000
   21.0180000000000
Box info found: 26.6770000000000 37.6080000000000
   33.4440000000000
Box info found: 15.4530000000000 33.0380000000000
   56.0720000000000
Box info found: 63.3550000000000 -18.3030000000000
  -6.55800000000000
Box info found: 74.8260000000000 59.5630000000000
   44.8510000000000
Box info found: 19.3560000000000 60.0230000000000
  -49.6850000000000
Box info found: 22.5590000000000 30.7510000000000
   46.3820000000000
Box info found: 63.7350000000000 25.4680000000000
   30.3630000000000
Box info found: 16.1750000000000 32.8380000000000
   14.6940000000000
Box info found: -8.00000000000000 36.8260000000000
   40.3520000000000
Box info found: 82.5740000000000 83.0840000000000
   73.7680000000000
Box info found: -8.52200000000000 21.3270000000000
   67.9200000000000
Box info found: 76.1750000000000 36.7570000000000
   96.0920000000000
Box info found: 74.5200000000000 32.6130000000000
   12.3730000000000
Box info found: 19.3890000000000 40.5950000000000
   10.9840000000000
Box info found: -29.5950000000000 76.4560000000000
   50.3060000000000
Box info found: 25.6000000000000 22.9470000000000
  -16.5670000000000
Box info found: 37.0410000000000 0.543000000000000
  -25.7030000000000
Box info found: 4.68700000000000 -7.49800000000000
   42.4970000000000
Box info found: -31.9060000000000 85.5290000000000
   54.1320000000000
Box info found: 59.4540000000000 31.2420000000000
   63.7750000000000
Box info found: 69.2210000000000 114.727000000000
   14.1210000000000
Box info found: 85.3960000000000 45.2510000000000
   16.8090000000000

3. binding_energy.mmpbsa

@GENERAL

PREFIX snapshot
PATH /home/bharatam/amberresults_w/amberresults31
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT /home/bharatam/amberresults_w/amb31/A31.prmtop
RECPT /home/bharatam/amberresults_w/amb31/A.prmtop
LIGPT /home/bharatam/amberresults_w/amb31/31.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#

@PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
FILLRATIO 4.0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@MM

DIELC 1.0
#
################################################################################
@GB
#
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@MS

#
PROBE 0.0
#
#################################################################################
@PROGRAMS

4. binding_energy.log

=>> Init
data
    Presuming executables of amber suite
to be in /opt/amber10/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH =>
/home/bharatam/amberresults_w/amberresults31
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT =>
/home/bharatam/amberresults_w/amb31/A31.prmtop
    Found RECPT =>
/home/bharatam/amberresults_w/amb31/A.prmtop
    Found LIGPT =>
/home/bharatam/amberresults_w/amb31/31.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 FILLRATIO => 4.0
    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
/home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.1
        Calc MM/GB/SAS

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