Dear AMBER users:
Two MD dynamics simulations (model A and model B) were performed for a
complex, just by changing the simulation condition. I list the result of
hydrogen bond and MM_PBSA in the below. You can see that the number of
hydrogen bonds of model A is much more than that of model B. however, in the
result of MM_PBSA, the ∆Eele and ∆Evdw of model A is lower than that of
model B. is it reasonable? Is there any another factors influence the
results? Thank you !
model A
model B
Hydrogen bond
Occupied
(%)
Hydrogen bond
Occupied
(%)
Ligand/Water
Residue/water
Ligand/Water
Residue/water
Ligand-O1
VAL123-O
90.48
Ligand-O1
GLU121-O
75.10
Ligand-O1
VAL123-N
97.72
Ligand-O5
PHE50-N
98.80
Ligand-O2
THR179-OG1
82.64
Ligand-O6
GLU90-OE2
100.00
Ligand-O5
PHE50-N
98.51
Ligand-N2
ASN171-OD1
72.70
Ligand-O6
GLU90-OE2
83.13
Ligand-O6
GLU90-OE1
36.90
Ligand-N2
ASP183-OD1
95.83
Ligand-O2
Wtr367-O(H1)
44.44
Ligand-O2
Wtr367-O(H2)
29.07
Wtr367-O(H1)
ASP183-OD1
28.57
Wtr367-O(H2)
ASP183-OD1
43.06
complex
code
ΔEele
ΔEvdw
ΔEgas
ΔEsur
ΔEcal
ΔEpbsol
ΔGcalc
C:ligand
A
-66.49
-66.10
-132.59
-5.47
115.40
109.93
-22.66
B
-68.38
-68.04
-136.32
-5.37
122.01
116.64
-19.68
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Received on Wed Jan 04 2006 - 18:16:50 PST
