Hi amber user audience,
I try to
calculate the binding energy interaction between a protein and a
peptide. But the calculated binding energy difference between the two
methods is so large, I am little bit confused which methods really give
significant results (please see the results below) . Secondly, the
experimental results is~10 kcal/mol. Hence it is hard to convince them the theoretical methodology works. I therefore, highly appreciate your comments and valuable suggestions. I
use AMBER 12.
MD input file
M1-Bec : 1 ns MD GB implicit solvent model
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 0,
igb = 7,
cut = 16.0,
ntr = 0,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
ig = -1,
nstlim = 500000, dt = 0.002
ntpr = 500, ntwx = 500, ntwr = 10000
/
Statistical out put
# DELTA
# -----------------------
# MEAN STD
#
=======================
ELE -277.70 24.61
VDW -103.33 5.44
INT 0.00 0.00
GAS -381.03 24.25
PBSUR -11.01 0.29
PBCAL 307.57 22.75
PBSOL 296.55
22.74
PBELE 29.87 9.40
PBTOT -84.48 8.73
GBSUR -11.01 0.29
GB 138.52 21.83
GBSOL 127.51 21.74
GBELE -139.17 18.69
GBTOT -253.52 16.08
binding-energy.mmpbsa
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT M11-bec.gas.prmtop
RECPT
M11.gas.prmtop
LIGPT beclin.gas.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 78.5
SCALE 2
LINIT
1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0050
CAVITY_OFFSET 0.00
SURFTEN 0.0050
SURFOFF 0.00
.MM
DIELC
1.0
.GB
IGB 7
GBSA 0
SALTCON 0.00
EXTDIEL 78.5
INTDIEL 1.0
SURFTEN 0.0050
SURFOFF 0.00
.MS
PROBE 0.0
.PROGRAMS
Thank you.
With best regards,
Delwar Hossain, Ph.D.
Department of Chemistry
and Biochemistry
North Dakota State University
Fargo, ND 58108
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Received on Wed Jun 06 2012 - 13:30:03 PDT
