AMBER Archive (2006)

Subject: AMBER: why has "ELE " a large fluctuation in MMPBSA?

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Jun 20 2006 - 08:56:25 CDT

Dear sir,
    I have a strange problem when I did MM_PBSA. My system is
protein-DNA-ligand complex. The receptor is protein-DNA complex, and the
ligand is a small molecule. I get 50 points from a stable 200 ps MD
simulation. In that simulation, it is obvious that energy for every step
in 200ps simulation don't change so much. However after I did MM_PBSA(I
only did MM section to test), I found "ELE " has a large fluctuation.
    Could you please give me some suggestion on it?
    In addition, I notice that Item INT for DELTA is not equal to O. What
problem could result in this mistake?

MD results:
-------------------------------------------------------------------------------------
       A V E R A G E S O V E R 100000 S T E P S

  NSTEP = 100000 TIME(PS) = 1200.000 TEMP(K) = 297.94 PRESS
= 1.0
  Etot = -1755294.9287 EKtot = 6319.6873 EPtot =
-1761614.6160
  BOND = 1374.4608 ANGLE = 5579.4236 DIHED =
2833.4301
  1-4 NB = 2212.7443 1-4 EEL = -5183.5817 VDWAALS =
-5710.5417
  EELEC = -1762720.5514 EHBOND = 0.0000 RESTRAINT =
0.0000
  EKCMT = 1.9203 VIRIAL = -24.2883 VOLUME =
1239972.2032
                                                     Density =
0.8688
  Ewald error estimate: 0.9679E+00
  ------------------------------------------------------------------------------

       R M S F L U C T U A T I O N S

  NSTEP = 100000 TIME(PS) = 1200.000 TEMP(K) = 2.04 PRESS =
51.9
  Etot = 3.7961 EKtot = 43.3440 EPtot =
45.1668
  BOND = 29.6708 ANGLE = 45.6035 DIHED =
26.7273
  1-4 NB = 13.7112 1-4 EEL = 38.6013 VDWAALS =
35.0353
  EELEC = 47.8923 EHBOND = 0.0000 RESTRAINT =
0.0000
  EKCMT = 0.9180 VIRIAL = 1390.4239 VOLUME =
142.3465
                                                     Density =
0.0001
  Ewald error estimate: 0.2632E-04

MMPBSA results:
-------------------------------------------------------------------------------------
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -23558.26 691.21 -23410.78 683.97
61.30 0.02
VDW -2745.00 28.83 -2730.24 29.06
16.89 0.01
INT 13160.44 52.99 13382.69 54.40
54.10 0.04
GAS -13142.81 696.51 -12758.34 689.12
132.29 0.03

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -208.78 64.66
VDW -31.64 3.68
INT -276.34 17.50
GAS -516.77 67.28
-----------------------------------------------------------------------
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