AMBER Archive (2004)

Subject: AMBER: Molecular dynamic

From: bybaker_at_itsa.ucsf.edu
Date: Wed Jul 07 2004 - 16:12:33 CDT

Hello, Amber

I tried to run molecular dynamic with my protein structural model using
Amber7. After the run, I notice that there are significant changes in
the structure. All the helix regions became partial unfolded. A
beta-sheet region connecting the N-terminal helix also turns to be
unfolded. I checked the energy (total, potential and kinetic) levels,
temperature, density & volume Vs. Time (ps) of the entire MD process
(including equilibration and production stages). All remained in stable
conditions after 20 ps run. And the mean pressure level is ~ 1 atm after
50 ps. All these data indicated that I had a successful MD run.
Furthermore, the RMSD level steady increased at first 20 ps, and was
gradually increasing during the rest of the run.

As a beginner of MD, I am not sure if I set the MD parameters and running
conditions properly. And I do not quite understand the results from my MD
run. Does it mean that these regions are quite flexible in solution?
>From the initial structure model, a salt-bridge was found to connect the
c-terminal helix and a loop region. After MD run, the salt-bridge was
still there despite the increased distance between C-helix and the loop.
>From related papers on line, most of them indicated that only minimal
conformational change observed with their MD runs. I went back to check
the template used for my structure modeling. The original crystal
structure template contains three MSE residues(?) in the helix regions.
And all these coordinate regions in my structure model turn into unfolded
after MD run. The MSE in the original crystal structure may have some
effects to stabilize the 3D-structure?

The follows are how I did with MD:

The structure was first solvated with ‘WATBOX216 10’ , and neutralizes
with 2 Na+. The water molecules were subjected 1000 steps minimization
followed by 1000 steps minimization on the entire system. The molecular
remained in the center of water shell after energy minimizations. MD was
performed for 0.5 ns after two steps of equilibrations.

Inputs for energy minimizations:

‘min1a.in’ for minimization water molecules:

Minimization solvates with cartesian restriantes for the solute
 &cntrl
   imin=1, ncyc=250, maxcyc=1000, ntpr=5,
 &end
Group input for restrained atoms
100.0
RES 1 220
END
END

‘min1b.in’ for minimization of entire system:
Energy minimization run 1a
 &cntrl
  imin=1, ncyc=250, maxcyc=1000, ntpr=5,
 &end

Inputs for MD runs:
‘1md.in’ for equilibration 1:

Initial molecular dynamic run 1: heating up the system, equilibration
stage 1:
 &cntrl
   imin=0, irest=0, ntx=1,
   ntt=1, tempi=100.0, temp0=300.0, tautp=2, ig=209858,
   ntp=0,
   ntb=1, ntc=2, ntf=2,
   nstlim=5000, dt=0.002,
   ntwr=5000, ntwx=5000, ntpr=500,
 &end

‘2md.in’ for equilibration 2:

Initial molrcular dynamic run 2: constant pressure constant temperature
equilibration stage 2
 &cntrl
  nstlim=5000, dt=0.002, ntx=7, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
 &end

‘md2.in’ for production run:
Initial molecular dynamic production run 1: constant pressure constant temp
 &cntrl
  nstlim=250000, dt=0.002, ntx=7, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
 &end

(from my last question posted about MD, I learned that the ‘ntx’ needs to
be set at ‘7’)

Would anyone please give me some advices on how to evaluate the result
from MD? Any any suggestions on my MD condtion settings?

Thank you in advance!

Sincerely

Bo Yang Baker

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