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×î½ü¿´ÁËһƪÂÛÎÄ£¬http://www.ncbi.nlm.nih.gov/pubmed/22339436
×÷ÕßʹÓÃamber×öÁËREMD£¨replica exchange molecular dynamic£©µÄ¼ÆËã¡£
×Ô¼ºÕýºÃÒ²ÓÐÀàËÆÐèÒª£¬ÏëÓÃREMDÄ£Äâ¡£¾ÍÏë°´ÂÛÎÄÏàͬµÄÌõ¼þʵÏÖһϣ¬²»¹ýÂÛÎÄÀïµÄ¹ý³ÌдµÄ²»ÊǺÜÏêϸ¡£ÏÂÃæÊÇÔ­ÎĵÄmethod²¿·Ö£º
In this work, the temperature setting used for sheep PrP 125-230 such that MD simulations were exchanged at 320.0, 322.0,324.0, 326.0, 328.1, 330.2, 332.3, 334.4, 336.5, 338.6, 340.8, 343.0, 345.2, 347.4, 349.6, 351.8, 354.0, 356.2, 358.5, 360.8, 363.1, 365.4, 367.7, and 370.0 K was used. All of the replicas were equilibrated for 20 ns without exchanging temperatures and then extended for 65 ns of REMD simulation. The generalized Born model used in this study modified the calculation of Born radii and improved the accuracy in the solvent polarization for macromolecules. The combinational use of the all-atom point-charge force-field (also known as ff03) and the generalized Born model led to successful folding of several proteins. The AMBER 11 simulation package 26 was used in both REMD simulation and data analysis. The melted huPrP 121-230 was computed starting from an extended huPrP. To generate the initial extended structure, a heating method was applied to a known NMR structure (PDBcode 1hjn,15Figure 1A), enabling it to unfold at 600 K for 40 ns of MD simulation to result in an extended conformation (Figure 1B) as described previously.
During this simulation, the disulfide covalent bond between residues 179 and 214 was preserved. In total, 24 replicas with duration of 65 ns and with an integration time step of 2 fs were computed based on the extended huPrP with different random number seeds to generate the initial conditions. A 16 Å force-shifted non-bonded cutoff and generalized Born solvent models with salt concentration of 0.2 M were applied.

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Simulation Procedure:
1.        system building
2.        system minimization
3.        heating system
4.        generate the extend conformation
5.        local minimization after heating system
6.        equilibrate the every replica
7.        REMD simulation


1.leap.inp for system building

source pdb: 1ag2
use the the ff03 (Duan et al.) force field

leap.inp

source leaprc.ff03.r1
# load pdb file
1ag2 = loadPdb input.pdb
# solvation
# solvatebox 1ag2 TIP3PBOX 18.0
# save 1ag2 to pdb file
savePdb 1ag2 1ag2.pdb
# add countinos
# addions 1ag2 Cl- 0
# addions 1ag2 Na+
# s-s bond
bond 1ag2.179.SG 1ag2.214.SG
# save 1ag2 to prmtop and inpcrd files
saveAmberParm 1ag2 1ag2.prmtop 1ag2.inpcrd
# finish
quit

2. system minimization
minimisation for heated system
&cntrl
  imin=1, maxcyc=1000, ncyc=500,
  cut=999., rgbmax=999.,igb=1, ntb=0,
  ntpr=100
/
~
~


3. heat the system

heating system from 0 K to 600K.
&cntrl
  nstlim = 50000, dt = 0.002,
  ntt = 1, tautp = 1.0,
  tempi = 0, temp0 = 600, ntc =2, ntf = 2,
  ntpr =100, ntwx = 100,
  ntb = 0, igb = 1,   #ÕâÀïÉèÖúͺóÃæremdµÄÉèÖò»Í¬£¨igb = 5£©½á¹û¿ÉÄÜÊÜÓ°Ïì¡£
  cut = 999.0,rgbmax = 999.0,
/

4. generate the full unfolded conformation

To generate the initial extend structure, a heating method was used to a known NMR structure (PDB code:1ag2), enabling it to unfold at 600 K for 40 ns of LD simulation to result in an extended conformation.

40nsld.inp
enabling the heated NMR structure to unfold at 600 K for 40ns of LD simulation
&cntrl
  irest = 1, ntx = 5,
  nstlim = 20000000, dt = 0.002,
  ntt = 3, gamma_ln = 1.0,
  tempi = 600,temp0 = 600,
  ntb = 0, igb = 2,
  ntpr = 500, ntwx = 1000, ntwr = 2000000,
  ntc = 2, ntf = 2,
  cut = 999.0,rgbmax = 999.0,
/
| RE_POSITION Moving by  -2.485812 -1.096141  0.618430

NSTEP = 20000000   TIME(PS) =   40060.000  TEMP(K) =   577.57  PRESS =     0.0
Etot   =      1351.4737  EKtot   =      2407.9819  EPtot      =     -1056.5082
BOND   =       626.4085  ANGLE   =      1429.4823  DIHED      =      1419.4285
1-4 NB =       376.4803  1-4 EEL =      3772.0639  VDWAALS    =      -368.8173
EELEC  =     -5949.1848  EGB     =     -2362.3695  RESTRAINT  =         0.0000
-------------------------------------------------------------------------
      A V E R A G E S   O V E R ******* S T E P S


NSTEP = 20000000   TIME(PS) =   40060.000  TEMP(K) =   600.20  PRESS =     0.0
Etot   =      1514.3153  EKtot   =      2502.2899  EPtot      =      -987.9746
BOND   =       644.7390  ANGLE   =      1506.2954  DIHED      =      1362.4635
1-4 NB =       397.8849  1-4 EEL =      3727.1078  VDWAALS    =      -361.6498
EELEC  =     -5967.0181  EGB     =     -2297.7973  RESTRAINT  =         0.0000
-------------------------------------------------------------------------
½á¹ûEptot µÄplotͼ   



600kmd.inp
enabling the heated NMR structure to unfold at 600 K for 40ns of LD simulation
&cntrl
  irest = 0, ntx = 1,
  nstlim = 20000000, dt = 0.002,
  ntt = 3, gamma_ln = 1.0,
  tempi = 600,temp0 = 600,
  ntb = 0, igb = 2,
  ntpr = 500, ntwx = 1000, ntwr = 2000000,
  ntc = 2, ntf = 2,
  cut = 999.0,rgbmax = 999.0,
/

600kmd.out
...
| RE_POSITION Moving by  -0.033675 -0.790281 -1.085325

NSTEP =  2000000   TIME(PS) =    4060.000  TEMP(K) =   601.00  PRESS =     0.0
Etot   =      1554.3820  EKtot   =      2505.6360  EPtot      =      -951.2540
BOND   =       654.9106  ANGLE   =      1485.1469  DIHED      =      1383.1021
1-4 NB =       422.1188  1-4 EEL =      3774.2620  VDWAALS    =      -379.3759
EELEC  =     -6038.4682  EGB     =     -2252.9505  RESTRAINT  =         0.0000
-------------------------------------------------------------------------
      A V E R A G E S   O V E R 2000000 S T E P S


NSTEP =  2000000   TIME(PS) =    4060.000  TEMP(K) =   599.90  PRESS =     0.0
Etot   =      1513.2011  EKtot   =      2501.0782  EPtot      =      -987.8771
BOND   =       644.5795  ANGLE   =      1506.1933  DIHED      =      1361.8286
1-4 NB =       398.1118  1-4 EEL =      3724.2906  VDWAALS    =      -363.4705
EELEC  =     -5968.1047  EGB     =     -2291.3058  RESTRAINT  =         0.0000


irest = 1, ntx = 5,ºÍirest = 0, ntx = 1 Ä£Äâ½á¹ý²î±ð»¹ÊÇÓе쬴ÓEPtotµÄ½á¹ûÀ´¿´£¬ºóÕ߽ṹ±ä»¯±È½Ï¼¤ÁÒ£¬Ç°Õß½ÏÎȶ¨¡£µ«ÊDz»ÖªµÀÔÚÕâ¸öÄ£ÄâÀïÓÃÄĸöºÏÊÊ£¿
5. local minimization after heating system

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6. equilibrate the every replica

equilibrate.mdin

equilibration 20 ns, every 10ps save output.
equilibration
&cntrl
   irest=0, ntx=1,
   nstlim=10000000, dt=0.002,
   irest=0, ntt=3, gamma_ln=1.0,
   temp0=XXXXX, ig=RANDOM_NUMBER,
   ntc=2, ntf=2, nscm=1000,
   ntb=0, igb=5,
   cut=999.0, rgbmax=999.0,
   ntpr=5000, ntwx=5000, ntwr=10000000,
   nmropt=1,
/
&wt TYPE='END'
/
DISANG=system_chir.dat

7.  REMD simulation
remd 40ns exchange every 2ps <- ÕâÀïÒ»Ö±ÓÐÀ§»ó£¬µ½µ×¼ä¸ô¶à¾Ã½»»»Ò»Ï±ȽϺÏÊÊ£¿
remd.mdin
remd 40ns exchange every 2ps
&cntrl
   irest=0, ntx=1,
   nstlim=1000, dt=0.002,
   irest=0, ntt=3, gamma_ln=1.0,
   temp0=XXXXX, ig=RANDOM_NUMBER,
   ntc=2, ntf=2, nscm=1000,
   ntb=0, igb=5,
   cut=999.0, rgbmax=999.0,
   ntpr=100, ntwx=1000, ntwr=100000,
   nmropt=1,
   numexchg=20000,
/
&wt TYPE='END'
/
DISANG=system_chir.dat
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2Â¥2013-07-03 09:54:58
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jackyma

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ÒýÓûØÌû:
3Â¥: Originally posted by 1054950560 at 2013-07-04 09:18:13
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jackyma

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Ëͺ컨һ¶ä
ÒýÓûØÌû:
2Â¥: Originally posted by ³¬ÈËÓëСľ³æ at 2013-07-03 09:54:58
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6Â¥2013-07-09 14:27:19
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2013-07-09 14:25   »Ø¸´  
ÒýÓûØÌû:
2Â¥: Originally posted by ³¬ÈËÓëСľ³æ at 2013-07-03 09:54:58 Ï£ÍûÄܹ»ÓëÄã½»Á÷½»Á÷£¡£¡£¡£¡

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