Hi All,
I am calculating the entropy contribution (10 snapshots) of
protein+ligand system using mm_pbsa.pl of amber12. I have used the
following input file
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./complex.prmtop
RECPT ./receptor.prmtop
LIGPT ./HI6.prmtop
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 1
.MAKECRD
BOX YES
NTOTAL 60464
NSTART 1
NSTOP 5000
NFREQ 500
NUMBER_LIG_GROUPS 1
LSTART 8247
LSTOP 8283
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 8246
.NM
DIELC 4
MAXCYC 20000
DRMS 0.1
IGB 1
PROC 1
SALTCON 0.0
INTDIEL 4.0
EXTDIEL 80.0
SURFTEN 0.0072
.TRAJECTORY
TRAJECTORY ./RES_md8.mdcrd
TRAJECTORY ./RES_md9.mdcrd
TRAJECTORY ./RES_md10.mdcrd
TRAJECTORY ./RES_md10_1.mdcrd
TRAJECTORY ./RES_md11.mdcrd
TRAJECTORY ./RES_md11_1.mdcrd
TRAJECTORY ./RES_md12.mdcrd
.PROGRAMS
The entropy value was calculated but the Std. deviation was very high
# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
TSTRA 17.61 0.00 17.61 0.00
12.85 0.00
TSROT 18.55 0.01 18.54 0.01
10.46 0.01
TSVIB 5627.70 42.86 5584.49 28.20
16.08 1.45
TSTOT 5663.86 42.87 5620.64 28.21
39.39 1.44
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -12.85 0.00
TSROT -10.45 0.02
TSVIB 27.13 61.08
TSTOT 3.83 61.09
snapshot_statistics.out lines 1-17/17 (END)
Then I made few changes in the input file. PROC =2, IGB=0.
The script is getting executed and finished but nothing is written to
the output file.
Note: I have already used mmpbsa.py script for the entropy calculations
Presently I am interested to calculate individual entropic
contribution of complex, receptor, and ligand using mm_pbsa.pl.
Instead of using single trajectory of the complex for the entropy
calculation. I am using separate trajectory files for complex,
receptor and ligand.
Can anybody suggest me the correct input files for the mm_pbsa.pl to run nmode ?
Thanks,
mani
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Received on Wed Jun 20 2012 - 09:00:03 PDT
