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From: JunJun Liu <ljjlp03.gmail.com>

Date: Tue, 20 Jun 2006 19:55:09 -0300

Dear Dr.Simmerling,

Thanks a lot for the responses. I may not state the problem clearly. In

this case, GB model is not used. What I did is like the followings:

1). MD simulation with explicit solvation box

2). extract snapshots from stable MD trajectory and remove waters and

counterions

3). Perform 1 step(single point) gas phase minimization against those

snapshots

I know the energy from MD simulation contains solvent contribution, and

this energy should be different with energy from gas phase. But it's

abnormal that the gas-phase electrostatic energy fluctuate too much, which

can be up to ~600kcal/mol. This is quite strange! We checked the RMSD of

selected snapshots, the values are less than 0.3A, indicating the selected

structures are very close! Any suggestions? Thanks!

Regards!

Liu

On Tue, 20 Jun 2006 20:10:48 -0300, Carlos Simmerling

<carlos.csb.sunysb.edu> wrote:

*> possible things to consider:
*

*>
*

*> 1) the GB solvated system is much smaller, so larger fluctuations are
*

*> expected (check
*

*> a stat mech book)
*

*> 2) you are calculating energies with a different energy function than
*

*> you used to
*

*> generate the simulation. It is entirely possible that the energy
*

*> fluctuations for the
*

*> trajectory from explicit water differ from what you would get if you
*

*> used structures
*

*> that were actually sampled in the GB model.
*

*> 3) the ele in the explicit water includes solvation, and the GB one does
*

*> not.
*

*> it is well known that these terms tend to fluctuate in the opposite
*

*> direction
*

*> so leaving the solvation energy out will give higher fluctuations.
*

*>
*

*>
*

*>
*

*> JunJun Liu wrote:
*

*>
*

*>> 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 <yxiong99.163.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
*

*>>> yxiong99.163.com
*

*>>> 2006-06-19
*

*>>>
*

*>>
*

*>>
*

*>>
*

*>
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

*> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
*

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Received on Wed Jun 21 2006 - 06:07:15 PDT

Date: Tue, 20 Jun 2006 19:55:09 -0300

Dear Dr.Simmerling,

Thanks a lot for the responses. I may not state the problem clearly. In

this case, GB model is not used. What I did is like the followings:

1). MD simulation with explicit solvation box

2). extract snapshots from stable MD trajectory and remove waters and

counterions

3). Perform 1 step(single point) gas phase minimization against those

snapshots

I know the energy from MD simulation contains solvent contribution, and

this energy should be different with energy from gas phase. But it's

abnormal that the gas-phase electrostatic energy fluctuate too much, which

can be up to ~600kcal/mol. This is quite strange! We checked the RMSD of

selected snapshots, the values are less than 0.3A, indicating the selected

structures are very close! Any suggestions? Thanks!

Regards!

Liu

On Tue, 20 Jun 2006 20:10:48 -0300, Carlos Simmerling

<carlos.csb.sunysb.edu> wrote:

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

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Received on Wed Jun 21 2006 - 06:07:15 PDT

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