A couple of questions here. Did you run mm_pbsa.pl previously in the same
folder without deleting the original output files? This error sometimes
occurs because mm_pbsa.pl output files are already present in the working
directory, so they are overwritten, causing these messages. You might want
to try deleting all mm_pbsa.pl files in your working directory and
re-running the calculation to see if that helps. Also, have you ran all of
the mm_pbsa.pl tests to make sure they all pass without this error?
Finally, these error messages are been mentioned on the Amber list many
times before, but the exact problem is often difficult to diagnose. As an
alternative, have you tried using MMPBSA.py instead?
-Bill
On Fri, Apr 8, 2011 at 1:58 AM, cwt <cwt_1986.163.com> wrote:
> 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!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Apr 08 2011 - 04:30:03 PDT
