AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Thu Jun 04 2009 - 16:00:51 CDT

Can you attach the output file for that error message? i.e.
"sander_com.1.out".

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/
==========================================

Vikas Sharma wrote:
> 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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>
>
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>

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