Dear all,
I have calculated the free energy with mm_pbsa/gbsa, but the results are very different.
the system is composed 342 residues protein complexed with a lysine ( with two amino groups,
one carboxylate, which doesn't exist in amber template, so the charge is fitted by resp method).
NTV minimization, and NTP molecular dynamics.
mm_pbsa.in as following:
_____________________________________________________________________________________
####PB Cal.
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2
LINIT 1000
BNDCON 4
CHARGE ../delphi.crg
SIZE ../delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.092
-----------------------------------------------------------------------------------------
###GB Cal.
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
----------------------------------------------------------------------------------------
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -9499.96 57.80 -8993.73 57.50 48.81 1.90
VDW -1497.10 30.52 -1478.84 30.07 0.66 0.70
INT 5734.94 46.53 5712.05 46.21 22.89 3.81
GAS -5262.11 66.63 -4760.51 67.54 72.36 3.78
PBSUR 85.83 1.05 86.61 1.03 1.05 0.01
PBCAL -4025.37 23.35 -4060.64 22.85 0.00 0.00
PBSOL -3939.54 22.97 -3974.02 22.47 1.05 0.01
PBELE -13525.33 44.88 -13054.37 44.82 48.81 1.90
PBTOT -9201.65 52.53 -8734.53 53.06 73.42 3.78
GBSUR 113.89 1.40 114.94 1.37 1.28 0.01
GB -6226.24 49.28 -6629.58 49.52 -137.64 2.82
GBSOL -6112.35 48.87 -6514.64 49.13 -136.36 2.82
GBELE -15726.20 40.88 -15623.31 39.48 -88.83 1.87
GBTOT -11374.46 44.00 -11275.15 41.98 -64.00 3.27
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -555.04 8.71
VDW -18.92 3.72
INT 0.00 0.00
GAS -573.96 7.15
PBSUR -1.84 0.07
PBCAL 35.26 2.01
PBSOL 33.43 2.00
PBELE -519.78 7.53
PBTOT -540.54 6.06
GBSUR -2.32 0.09
GB 540.98 6.69
GBSOL 538.66 6.69
GBELE -14.06 6.31
GBTOT -35.30 4.41
Who could give me a hand?
Thanks in advance.
Yongjun Jiang
yjjiang_at_mail.shcnc.ac.cn
2002-09-10
Received on Tue Sep 10 2002 - 00:18:46 PDT
