Dear Amber users,
I try to calculate the binding energy using both GB and PB models of amber8 mm-pbsa program. My calculation stopped at ¡®=>> Calc delta from raw data¡¯ and gave some wrong information such as ¡®No values for MM_GAS existing -> Skipping¡¯. The mm_pbsa.in and mm_pbsa.out file are listed as follow. I highly appreciate ones who have the similar experience and can give me some advice.
Thanks in advance!
Bing Liu
mm_pbsa.in
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 08.02.2002
#
################################################################################
.GENERAL
#
PREFIX DHPL-KES
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./complex.top
RECPT ./receptor.top
LIGPT ./ligand.top
#
GC 1
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 1.6
#
RADIOPT 0
#
FOCUS 0
PERFIL 80.0
CHARGE /home/program/amber8/src/mm_pbsa/Examples/my_amber94_delphi.crg
SIZE /home/program/amber8/src/mm_pbsa/Examples/my_parse_delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.092
#
#
################################################################################
.MM
#
#
DIELC 1.0
#
################################################################################
.GB
#
IGB 1
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
PROBE 1.4
#
##################################################################################
.NM
#
DIELC 4
MAXCYC 10000
DRMS 0.0001
#
#################################################################################
.MAKECRD
#
BOX NO
NTOTAL 4135
NSTART 1
NSTOP 200
NFREQ 100
#
NUMBER_LIG_GROUPS 1
LSTART 4105
LSTOP 4135
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 4104
#
#################################################################################
.TRAJECTORY
#
TRAJECTORY ../DHPL-KES.md_stripped.xx
#
###############################################################################
.PROGRAMS
#
DELPHI /home/program/delphi/delphi
#
mm_pbsa.out
=>> Init data
Presuming executables of amber suite to be in /home/program/amber8/exe
=>> Reading input parameters
Found PREFIX => DHPL-KES
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./complex.top
Found RECPT => ./receptor.top
Found LIGPT => ./ligand.top
Found GC => 1
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 => 1.6
Found RADIOPT => 0
Found FOCUS => 0
Found PERFIL => 80.0
Found CHARGE => /home/program/amber8/src/mm_pbsa/Examples/my_amber94_delphi.crg
Found SIZE => /home/program/amber8/src/mm_pbsa/Examples/my_parse_delphi.siz
Found SURFTEN => 0.00542
Found SURFOFF => 0.092
Found DIELC => 1.0
Found IGB => 1
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 => 1.4
Found RADII => ./atmtypenumbers
Found DIELC => 4
Found MAXCYC => 10000
Found DRMS => 0.0001
Found BOX => NO
Found NTOTAL => 4135
Found NSTART => 1
Found NSTOP => 200
Found NFREQ => 100
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 4105
Found LSTOP => 4135
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 4104
Found TRAJECTORY => ../DHPL-KES.md_stripped.xx
Found DELPHI => /home/program/delphi/delphi
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
make_crd input
=>> Creating coordinates
Executing makecrd
Amber8 Module: make_crg_hg
usage: make_crd_hg < trajectory_file
=>> Calculating energy / entropy contributions
Calc contrib for ./DHPL-KES_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./DHPL-KES_com.crd.2
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./DHPL-KES_rec.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./DHPL-KES_rec.crd.2
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./DHPL-KES_lig.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./DHPL-KES_lig.crd.2
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.00542
betaP = 0.092
gammaG = 0.0072
betaG = 0.00
=>> Reading input
=>> Reordering files
Final order:
1. DHPL-KES_com.all.out: -
2. DHPL-KES_rec.all.out: -
3. DHPL-KES_lig.all.out: -
=>> Reading files
Reading DHPL-KES_com.all.out
WARNING: Missing SURF for MS in 0 -> Taken from -1
WARNING: Missing SURF for MS in 1 -> Taken from 0
Reading DHPL-KES_rec.all.out
Checking CALC
WARNING: Missing SURF for MS in 0 -> Taken from -1
WARNING: Missing SURF for MS in 1 -> Taken from 0
Reading DHPL-KES_lig.all.out
Checking CALC
=>> Treat special parameters
=>> Calc missing parameters
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 GAS
Doing 1 MM ELE
Doing 1 MM VDW
No values for MM_VDW 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 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 PBCAL
Doing 1 PB PBSUR
Doing 1 PB PBCAL
Doing 1 PB PBSUR
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
---------------------------------
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Received on Sun Feb 19 2006 - 06:10:07 PST
