AMBER Archive (2006)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Jun 20 2006 - 18:48:54 CDT

> 1) the GB solvated system is much smaller, so larger fluctuations are
> expected (check a stat mech book)

As Professor Simmerling points out, the larger the system, the smaller the
fluctuation in energy. Moreover, the energy in the water solvated case is
huge (favorable) and dominated by water-water interaction (such that
fluctuations in protein-DNA energy are hidden in the noise).

To see how fluctuations for a smaller system go, consider this DNA duplex
(15-mer) molecular dynamics run with GB. One might expect that a MM-PBSA
analysis would show even larger fluctuations (due to differences in the
potential, point (2) of Simmerling):

       A V E R A G E S O V E R 4500000 S T E P S

  NSTEP = 9000000 TIME(PS) = 510455.000 TEMP(K) = 308.55 PRESS = 0.0
  Etot = -4930.8310 EKtot = 769.1995 EPtot = -5700.0306
  BOND = 273.6632 ANGLE = 536.5876 DIHED = 543.2981
  1-4 NB = 214.0047 1-4 EEL = -3246.6619 VDWAALS = -101.4745
  EELEC = 826.7482 EGB = -4746.1959 RESTRAINT = 0.0000

------------------------------------------------------------------------------

       R M S F L U C T U A T I O N S

  NSTEP = 9000000 TIME(PS) = 510455.000 TEMP(K) = 8.78 PRESS = 0.0
  Etot = 1266.6986 EKtot = 21.8931 EPtot = 1266.4548
  BOND = 14.3338 ANGLE = 18.5960 DIHED = 14.7850
  1-4 NB = 5.5145 1-4 EEL = 23.7982 VDWAALS = 4.8822
  EELEC = 1267.0361 EGB = 141.9796 RESTRAINT = 0.0000

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

Looking at your MMPBSA results, I am somewhat surprised by the rather
large INT which represents the bond, angle and dihedral contributions in
the receptor... I would try to figure out where this is coming from
(perhaps by using anal on a single frame from the trajectory). However,
if this were due to a problem with the coordinates (i.e. incorrect
stripping or coordinate mismatch or some such), likely the VDW and ELE
terms would be highly unfavorable. It is always wise to visualize the
trajectory being processed to see if it makes sense.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu