amber tutorial part 2

assalamu’alaikum warahmatullahi wabarakatuh..

 

melanjutkankan pembahasan bagian pertama mengenai tutorial sederhana di AMBER. kali ini kita akan mencoba membuat kotak simulasi AMBER yang berisi protein dan air.

source leaprc.ff99SB

source leaprc.gaff

loadoff S2P.off

loadamberparams S2P.frcmod

mol=loadpdb peptida_md.pdb

solvatebox mol SPCBOX 14 iso -> memasukkan air model SPC ke kotak simulasi kubus dengan jarak antara solute dengan rusuk kotak 14 angstroems

saveamberparm mol mol_box.prmtop mol_box.inpcrd

kotak ini kemudian dapat dilakukan minimasi

peptide : initial minimization solvent

&cntrl

imin = 1,

maxcyc = 1000,

ncyc = 500, (500 steepest descent min, followed by 500 steps conjugate gradient)

ntb = 1, (periodic boundary)

ntr = 1, (position restraints on)

cut = 10.0 (cutoff)

/

Hold the peptide fixed

500.0 (500 kcal/mol force constant)

RES 1 14

END

END

untuk minimasi kedua

peptide and la explicit: initial minimization whole system

&cntrl

imin = 1,

maxcyc = 2500,

ncyc = 1000, (1000 cycles steepest descent)

ntb = 1, (periodic boundary)

ntr = 0, (no position restraints)

cut = 15.0 (cutoff)

/

 

dan terakhir bisa kita coba melakukan simulasi dinamika molekular

peptide: 20ps MD with res on peptide

&cntrl

imin = 0, (minimization is off)

irest = 0, (random initial velocities)

ntx = 1, (random initial velocities)

ntb = 1, (periodic boundary on)

cut = 14.0, (cutoff)

ntr = 1, (position restraints)

ntc = 2, (shake is on)

ntf = 2, (shake is on)

tempi = 0.0,

temp0 = 300.0,

ntt = 3, (langevin dynamics)

gamma_ln = 1.0, (langevin dynamics with collision frequency of 1ps)

nstlim = 10000, dt = 0.002 (10000 molecular dynamics steps with 2 fs time step)

ntpr = 100, ntwx = 100, ntwr = 1000 (output every 100 steps, trajectory and restart file every 100 steps, in case our job crashes and we want to restart it, every 1,000 steps)

/

Keep peptide fixed with weak restraints

10.0

RES 1 14

END

END

 

Oke, cukup sekian dan semoga bermanfa’at !

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