Dear Amber users
I am not getting the results for mmpbsa calculation Calculate the
binding free energy. Can anyone help me?
I have
given both my input and output files.
This is my input
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./GNNQQNYMYRSB.prmtop
RECPT ./GNNQQNYSB.prmtop
LIGPT ./MYR.prmtop
GC 0
AS 0
DC 0
MM 1
GB 2
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
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
This is my Out put
=>> Init data
Presuming executables of amber suite to be in /u0/z/zz217/USG/amber/9.0/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./GNNQQNYMYRSB.prmtop
Found RECPT => ./GNNQQNYSB.prmtop
Found LIGPT => ./MYR.prmtop
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 2
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 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
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
/u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o
pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not
successful
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Received on Wed Aug 19 2009 - 22:33:23 PDT
