Dear AMBER users,
I am calculating the binding free energy of a complexed protein-ligand system
using binding_energy.mmpbsa (from AMBER tutorial) .
The snapshots seem to be extracted correctly with appropriate box information in
the log file.
However while calculating the binding energy with the command below, it shows
the following message:
/usr/apps/amber10/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
/usr/apps/amber10//exe/ambpdb -p
/data/Making_TOP-files/apo-gas-protonated.top <
/data/EXTR_CRD/snapshot_rec.crd.1 > tmp.pdb 2> /dev/null not successful
Also the tmp.pdb file generated has the message like
Unit 10 Error on OPEN: /data/Making_TOP-files/apo-gas-prot
I understand that, the system is not recognizing the apo-gas-protonated.top file
from its mentioned path. However I checked the file path and also the top file,
which seems to be fine. I couldn't understand what is going wrong here.
FYI, I have copied the contents of binding_energy.log file in this text. please
check it below.
=>> Init data
Presuming executables of amber suite to be in /usr/apps/amber10//exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => /data/EXTR_CRD
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => /data/COM-prot-gas-Noions.top
Found RECPT => /data/Making_TOP-files/apo-gas-protonated.top
Found LIGPT => /data/Making_TOP-files/LIG-only-gas.top
Found GC => 0
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 => 1.4
Found ISTRNG => 0.0
Found RADIOPT => 0
Found NPOPT => 1
Found CAVITY_SURFTEN => 0.00542
Found CAVITY_OFFSET => 0.92
Found SURFTEN => 0.00542
Found SURFOFF => 0.92
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.00542
Found SURFOFF => 0.92
Found PROBE => 0.0
=>> Checking sanity
Checking GENERAL
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Calc MS
Calc contrib for /data/EXTR_CRD/snapshot_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
;
;
;
;
;
Calc contrib for /data/EXTR_CRD/snapshot_com.crd.50
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for /data/EXTR_CRD/snapshot_rec.crd.1
Calc MM/GB/SAS
Generate PDB
It seems from the log file that the script is running fine for the complex , but
while calculating for the individual receptor, it is failed.
Can anyone suggest me how to overcome this problem.
Thanks
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Received on Fri Feb 04 2011 - 16:00:05 PST
