Hello Amber users,
I'm using mm_pbsa.pl of Amber 10 to calculate free binding energy of my system. But I gained only three out files, snapshot_lig.all, snapshot_rec.all, and snapshot_com.all. I got records in binding_energy.log file as follows:
=>> Reading files
Reading snapshot_com.all.out
Entry 0 MM BOND 0 exists -> overwriting
Entry 0 MM DIHED 0 exists -> overwriting
Entry 0 MM ANGLE 0 exists -> overwriting
Entry 0 MM ELENB 0 exists -> overwriting
Entry 0 MM VDWNB 0 exists -> overwriting
Entry 0 GB GB 0 exists -> overwriting
Entry 0 MM ELE14 0 exists -> overwriting
Entry 0 MM VDW14 0 exists -> overwriting
WARNING: Missing BOND for MM in 1 -> Taken from 0
WARNING: Missing ELE14 for MM in 1 -> Taken from 0
WARNING: Missing ELENB for MM in 1 -> Taken from 0
WARNING: Missing VDWNB for MM in 1 -> Taken from 0
WARNING: Missing DIHED for MM in 1 -> Taken from 0
WARNING: Missing ANGLE for MM in 1 -> Taken from 0
WARNING: Missing VDW14 for MM in 1 -> Taken from 0
WARNING: Missing GB for GB in 1 -> Taken from 0
WARNING: Missing PB for PB in 1 -> Taken from 0
WARNING: Missing PBCAV for PB in 1 -> Taken from 0
WARNING: Missing PBDIS for PB in 1 -> Taken from 0
WARNING: Missing SURF for MS in 1 -> Taken from 0
WARNING: Missing BOND for MM in 2 -> Taken from 1
WARNING: Missing ELE14 for MM in 2 -> Taken from 1
WARNING: Missing ELENB for MM in 2 -> Taken from 1
WARNING: Missing VDWNB for MM in 2 -> Taken from 1
WARNING: Missing DIHED for MM in 2 -> Taken from 1
WARNING: Missing ANGLE for MM in 2 -> Taken from 1
WARNING: Missing VDW14 for MM in 2 -> Taken from 1
WARNING: Missing GB for GB in 2 -> Taken from 1
WARNING: Missing PB for PB in 2 -> Taken from 1
WARNING: Missing PBCAV for PB in 2 -> Taken from 1
WARNING: Missing PBDIS for PB in 2 -> Taken from 1
WARNING: Missing SURF for MS in 2 -> Taken from 1
WARNING: Missing BOND for MM in 3 -> Taken from 2
WARNING: Missing ELE14 for MM in 3 -> Taken from 2
WARNING: Missing ELENB for MM in 3 -> Taken from 2
WARNING: Missing VDWNB for MM in 3 -> Taken from 2
WARNING: Missing DIHED for MM in 3 -> Taken from 2
WARNING: Missing ANGLE for MM in 3 -> Taken from 2
WARNING: Missing VDW14 for MM in 3 -> Taken from 2
WARNING: Missing GB for GB in 3 -> Taken from 2
WARNING: Missing PB for PB in 3 -> Taken from 2
WARNING: Missing PBCAV for PB in 3 -> Taken from 2
WARNING: Missing PBDIS for PB in 3 -> Taken from 2
WARNING: Missing SURF for MS in 3 -> Taken from 2
Entry 0 MM BOND 4 exists -> overwriting
Entry 0 MM DIHED 4 exists -> overwriting
Entry 0 MM ANGLE 4 exists -> overwriting
Entry 0 MM ELENB 4 exists -> overwriting
Entry 0 MM VDWNB 4 exists -> overwriting
Entry 0 GB GB 4 exists -> overwriting
Entry 0 MM ELE14 4 exists -> overwriting
Entry 0 MM VDW14 4 exists -> overwriting
Entry 0 MM BOND 4 exists -> overwriting
Entry 0 MM DIHED 4 exists -> overwriting
Entry 0 MM ANGLE 4 exists -> overwriting
Entry 0 MM ELENB 4 exists -> overwriting
Entry 0 MM VDWNB 4 exists -> overwriting
Entry 0 GB GB 4 exists -> overwriting
Entry 0 MM ELE14 4 exists -> overwriting
Entry 0 MM VDW14 4 exists -> overwriting
Entry 0 MM BOND 4 exists -> overwriting
Entry 0 MM DIHED 4 exists -> overwriting
Entry 0 MM ANGLE 4 exists -> overwriting
Entry 0 MM ELENB 4 exists -> overwriting
Entry 0 MM VDWNB 4 exists -> overwriting
Entry 0 GB GB 4 exists -> overwriting
Entry 0 MM ELE14 4 exists -> overwriting
Entry 0 MM VDW14 4 exists -> overwriting
Reading snapshot_rec.all.out
Checking consistency of CALC
Checking consistency of DATA
Reading snapshot_lig.all.out
Checking consistency of CALC
Checking consistency of DATA
=>> Values of parameters
TEMP = 300
R = 8.314
gammaP = 0.0072
betaP = 0.00
gammaG = 0.0072
betaG = 0.00
=>> 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
There's no snapshot_statistics.out file in my folder.I don' know what causes this. ps. I have fixed all th bugs in Amber10.
Thank you!
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Received on Thu Apr 07 2011 - 23:00:02 PDT
