Hello,
I have AMBER16 and I am using mm_pbsa.pl to calculate the free binding
energy of a receptor and protein.
I am receiving the following error messages in the binding_energy.log file
when running binding_energy calculations for mm_pbsa.pl:
-- =>> Doing statistics
=>> Reading input
=>> Reordering files
Final
order:
1. snapshot_com.all.out: -
2. snapshot_rec.all.out: -
3. snapshot_lig.all.out:
-
=>> Reading files
Reading snapshot_com.all.out
WARNING: Missing PBCAV for PB in 84 -> Taken from
83
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
WARNING: Missing PBDIS for PB in 84 -> Taken from 83
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
WARNING: Missing SURF for MS in 84 -> Taken from 83
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
=>> Values of parameters
TEMP = 300
R = 8.314
gammaP = 0.005
betaP = 0.00
gammaG = 0.005
betaG = 0.00
=>> Treat special parameters
=>> Calc missing parameters
Processing MM GAS
Doing 1 MM ELE
No values for MM_ELE existing -> Skipping
For details see:
http://ambermd.org/Questions/mm_pbsa.html#calc_missing_no_value_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
Doing 1 GB GBSOL
No values for GB_GBSOL existing -> Skipping
For details see:
http://ambermd.org/Questions/mm_pbsa.html#calc_missing_no_value_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
For details see:
http://ambermd.org/Questions/mm_pbsa.html#calc_missing_no_value_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+1 MM BOND 1000
For details see:
http://ambermd.org/Questions/mm_pbsa.html#calc_delta_no_data_plus_one
The mmpsa errors link says that " No data for 0+1 MM BOND 1000" means that
the script might be mixing up files from previous runs that are present in
the directory. I reran the job in a new directory and received the same
error messages. My system consists of a 290 residue receptor and a 350
residue protein. This error consistently appears when trying to run
mm_pbsa.pl for 750 and 1000 mdcrd trajectory analysis. I have successfully
ran mm_pbsa.pl for the exact same system using a 250 mdcrd trajectory. The
prmtop files and atom masks in the extract_coords.mmpbsa file are all
correct because the previous 250 mdcrd trajectory gave me good results. My
input binding_energy.mmpbsa file is shown below.
.GENERAL
VERBOSE 0
PARALLEL 0
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
ISTRNG 0.0
RADIOPT 0
ARCRES 0.0625
INP 1
SURFTEN 0.005
SURFOFF 0.00
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.005
SURFOFF 0.00
.MS
PROBE 0.00
I hope I provided enough information, I look forward to your feedback.
Best regards,
Luis J. Santiago
RISE Fellow
Research Assistant
Undergraduate l Department of Biology | College of Science and Mathematics
California State University, Northridge
luis.jaimes.871.my.csun.edu
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Received on Wed May 01 2019 - 18:00:02 PDT
