hello all
I have been facing the problem with the binding free energy calculation
with MMPBSA
while using the following script I was able to successfully carry out
binding free energy for two snapshot
however when I tried to perform the analysis for larger number of snapshot
the process died while carrying calculation of snapshot pertaining to ligand
Initially I tried to perform calculation by taking 2 snapshot starting from
1 upto 2
It worked well but failed when the 21 snapshots were taken for which the the
range selected was from 400-420 but it failed.
I am using amber 10
*
**my extract_coords.mmpbsa*
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./gsk-ref.prmtop
RECPT ./gsk-nn.prmtop
LIGPT ./lig.prmtop
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
BOX YES
NTOTAL 55388
NSTART 400
NSTOP 420
NFREQ 1
#
NUMBER_LIG_GROUPS 1
LSTART 5669
LSTOP 5702
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 5668
TRAJECTORY ./prod.mdcrd
*
last few lines from my binding_energy.log file *
Calc contrib for ./snapshot_rec.crd.20
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_rec.crd.21
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_lig.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
any help would be highly obliged
--
Regards:
Juzer Stationwala,
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education & Research
(NIPER)
Mohali,
Punjab.
India
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Received on Sun Sep 26 2010 - 08:00:05 PDT
