Dear Members,
When I use pbsa.in script for binding energy calculations, I
have an error like this:
Binding energy calculations stops after reading the first
snapshot it never proceed after that step. Here is part of
binding_energy.log file
=>> Calculating energy / entropy contributions
Calc contrib for ../EXTRA_COORDS/snapshot_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ../EXTRA_COORDS/snapshot_com.crd.2
Calc MM/GB/SAS
I can’t understand what could be the error? Could you
please suggest me what could be the error and how to solve
it?
Here is my binding_energy_mmpbsa file
.GENERAL
PREFIX snapshot
PATH ../EXTRA_COORDS/
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ../4FVC_62_NCW.prmtop
RECPT ../4FVC_nCW.prmtop
LIGPT ../LIG.prmtop
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
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
SANDER $AMBERHOME/exe/sander
.PROGRAMS
Thanks.
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Received on Wed Apr 18 2007 - 06:07:22 PDT
