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From: Biao Ma <jackyma1981.gmail.com>

Date: Thu, 4 Jul 2013 09:47:32 +0900

Hello, amber users,

Now, I am reading a paper that is "Insights into structural properties of

denatured human prion 121-230 at melting temperature studied by replica

exchange molecular dynamics". Base on the describe of paper, I write the

process and the input file of amber simulation, but I cannot sure that is

correct.****

Who can help me check it?****

**

Thank a lot.

Biao Ma

**

pumed url of the paper: http://www.ncbi.nlm.nih.gov/pubmed/22339436****

** **

Blow is a part of method in the paper:****

=====start

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.****

**=====end

**

**

**

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****

set default PBradii mbondi2****

# load pdb file****

1ag2 = loadPdb input.pdb****

savePdb 1ag2 1ag2.pdb****

bond 1ag2.179.SG <http://1ag2.179.sg/> 1ag2.214.SG <http://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,****

igb=5, ntb=0,****

cut = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=100****

/****

~****

~****

** **

*3. heat the system*

heating system from 0 K to 600K during 100 ps.****

&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 = 5, ****

cut = 16, rgbmax = 16, saltcon = 0.2,****

nmropt = 1,****

/****

&wt****

type = 'TEMP0', istep1 = 0, istep2 =50000, value1 = 0, value2=600,****

/****

&wt type = 'END'****

/****

** **

*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.****

here, I do not sure whether I do the restart MD(set irest = 1, ntx = 5, or

irest = 0, ntx = 1), Simulation results is difference, which setting should

I use?

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 = 5,****

ntpr = 500, ntwx = 1000, ntwr = 2000000,****

ntc = 2, ntf = 2,****

cut = 16, rgbmax = 16, saltcon = 0.2,****

/

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 = 16, rgbmax = 16, saltcon = 0.2,****

/

40nsld.out irest = 1, ntx = 5,****

600kmd.out irest = 0, ntx = 1****

[image: 40nsld.etot.png]****

[image: 600kmd.etot.png]

** **

5. local minimization after heating system****

use the mdin file which is same to step 3 above。****

** **

6. equilibrate the every replica****

** **

equilibrate.mdin****

** **

equilibration 20 ns, every 10ps save output. <- Is this must to do

equilibrate for 20 ns?**

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 = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=5000, ntwx=5000, ntwr=10000000,****

nmropt=1,****

/****

&wt TYPE='END'****

/****

DISANG=system_chir.dat****

** **

7. REMD simulation****

remd 65ns exchange every 2ps <- Here I have been confused, how often to

exchange is more appropriate ?****

** **

remd.mdin****

remd 65ns 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 = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=100, ntwx=1000, ntwr=100000,****

nmropt=1,****

numexchg=32500,****

/

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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jul 03 2013 - 18:00:02 PDT

Date: Thu, 4 Jul 2013 09:47:32 +0900

Hello, amber users,

Now, I am reading a paper that is "Insights into structural properties of

denatured human prion 121-230 at melting temperature studied by replica

exchange molecular dynamics". Base on the describe of paper, I write the

process and the input file of amber simulation, but I cannot sure that is

correct.****

Who can help me check it?****

**

Thank a lot.

Biao Ma

**

pumed url of the paper: http://www.ncbi.nlm.nih.gov/pubmed/22339436****

** **

Blow is a part of method in the paper:****

=====start

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.****

**=====end

**

**

**

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****

set default PBradii mbondi2****

# load pdb file****

1ag2 = loadPdb input.pdb****

savePdb 1ag2 1ag2.pdb****

bond 1ag2.179.SG <http://1ag2.179.sg/> 1ag2.214.SG <http://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,****

igb=5, ntb=0,****

cut = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=100****

/****

~****

~****

** **

*3. heat the system*

heating system from 0 K to 600K during 100 ps.****

&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 = 5, ****

cut = 16, rgbmax = 16, saltcon = 0.2,****

nmropt = 1,****

/****

&wt****

type = 'TEMP0', istep1 = 0, istep2 =50000, value1 = 0, value2=600,****

/****

&wt type = 'END'****

/****

** **

*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.****

here, I do not sure whether I do the restart MD(set irest = 1, ntx = 5, or

irest = 0, ntx = 1), Simulation results is difference, which setting should

I use?

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 = 5,****

ntpr = 500, ntwx = 1000, ntwr = 2000000,****

ntc = 2, ntf = 2,****

cut = 16, rgbmax = 16, saltcon = 0.2,****

/

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 = 16, rgbmax = 16, saltcon = 0.2,****

/

40nsld.out irest = 1, ntx = 5,****

600kmd.out irest = 0, ntx = 1****

[image: 40nsld.etot.png]****

[image: 600kmd.etot.png]

** **

5. local minimization after heating system****

use the mdin file which is same to step 3 above。****

** **

6. equilibrate the every replica****

** **

equilibrate.mdin****

** **

equilibration 20 ns, every 10ps save output. <- Is this must to do

equilibrate for 20 ns?**

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 = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=5000, ntwx=5000, ntwr=10000000,****

nmropt=1,****

/****

&wt TYPE='END'****

/****

DISANG=system_chir.dat****

** **

7. REMD simulation****

remd 65ns exchange every 2ps <- Here I have been confused, how often to

exchange is more appropriate ?****

** **

remd.mdin****

remd 65ns 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 = 16, rgbmax = 16, saltcon = 0.2,****

ntpr=100, ntwx=1000, ntwr=100000,****

nmropt=1,****

numexchg=32500,****

/

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