AMBER Archive (2006)

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

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Jun 20 2006 - 16:37:52 CDT

Hi all,

It's acutally a sander related problem. The sander program produces a
stable trajectory when performing a MD simulation in explicit water box,
but gives out very unstable energy curve if doing vacuum single-point
energy calculation against snapshots of this MD trajectory(with waters and
counterions removed). What could be the reason? Since it's a DNA+Protein
system, does this mean the force field(ff99) can't describe the system
well? Or caused by other problem? Any suggestions? Thanks!

Regards!

Liu

On Tue, 20 Jun 2006 10:47:44 -0300, yxiong99 <yxiong99_at_163.com> wrote:

> 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
> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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