AMBER Archive (2005)

Subject: AMBER: does the result of H bond is consistent with the ∆Eele of MM_PBSA?

From: haixiao jin (jinhx952_at_gmail.com)
Date: Thu Dec 22 2005 - 22:12:46 CST

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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