Dear All :
I'm sorry for sending this mail again, I still can't solve this problem by now, hope someone kind enough to give me some advices. After run a short time simulation, I got the value of the binding energy. But it seems wrong, the PBTOT is positive.This indicates that my system is not stable.The structure is good by using VMD. My input file is below.I am confused about this, Could someone tell me how to solve this problem?
BTW,there is a metal ion near the ligand,the distance is about 5A. I used the bonded model and resp charge to simulate the meatal ion. when I prapared the initial prmtop fiel for the MMPBSA, I treat the protein and the metal ion as the receptor and I still use the bonded model+resp charge (eg,the charge of the metal ion is not integral ,it is 0.6e....). I don't know if is this caused the strange value.Could someone help me?Thank you very much!
my input file:
PREFIX snapshot
PATH ../snap/
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./111.prmtop
RECPT ./222.prmtop
LIGPT ./333.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
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
.PROGRAMS
My ouput file:
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -14104.08 118.29 -14214.13 117.48 6.36 4.11
VDW -2952.56 34.85 -2902.22 34.50 6.00 2.05
INT 12956.05 80.78 12881.95 80.06 66.38 5.11
GAS -4100.59 126.66 -4234.41 125.40 78.74 7.00
PBSUR 174.96 2.55 176.25 2.47 5.11 0.05
PBCAL -6431.77 111.16 -6315.64 109.09 -74.51 3.51
PBSOL -6256.81 109.58 -6139.40 107.60 -69.40 3.52
PBELE -20535.85 48.06 -20529.78 47.63 -68.15 1.00
PBTOT -10357.40 84.52 -10373.81 83.73 9.34 5.07
GBSUR 174.96 2.55 176.25 2.47 5.11 0.05
GB -6603.77 108.13 -6473.90 106.79 -76.45 3.77
GBSOL -6428.81 106.76 -6297.65 105.47 -71.34 3.78
GBELE -20707.85 37.14 -20688.04 37.02 -70.09 0.84
GBTOT -10529.40 77.15 -10532.06 76.75 7.40 5.10
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 103.69 11.46
VDW -56.34 2.74
INT 7.73 2.46
GAS 55.08 10.76
PBSUR -6.40 0.31
PBCAL -41.62 11.08
PBSOL -48.01 11.00
PBELE 62.08 5.34
PBTOT 7.06 4.49
GBSUR -6.40 0.31
GB -53.42 9.80
GBSOL -59.82 9.75
GBELE 50.27 3.57
GBTOT -4.74 3.27
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Received on Sat Nov 13 2010 - 20:30:05 PST
