AMBER Archive (2006)

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

From: yxiong99 (yxiong99_at_163.com)
Date: Tue Jun 20 2006 - 08:47:44 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?
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

　　　　　　　　Ying Xiong
　　　　　　　　yxiong99_at_163.com
　　　　　　　　　　2006-06-19
 
 
 
 
 
 
 
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