0307.trpzip2.org

simulate

trpzip2

compute with cpu RMSD

Temperature constraint

no constraint

exist constraint

explicit

CLN025

explicit

Prepare

Method

• Force Field ff12SB
• Solvateoct TIP3PBOX

tleap

source leaprc.protein.ff12SB
mol=sequence {NSER TRP THR TRP GLU ASN GLY LYS TRP THR TRP CLYS}
source leaprc.water.tip3p
solvateoct mol TIP3PBOX 8
addions2 mol Cl- 0
saveamberparm mol trpzip2_solv.prmtop trpzip2_solv.inpcrd
quit

minimize

Hold protein fixed

stage 1 minimize
&cntrl
imin=1,maxcyc=10000,ncyc=5000,
cut=10.0,ntc=2,ntf=2,ntb=1,ntr=1
/
Hold protein fixed
500.0
RES 1 12
END
END

Relax everything

stage 1 minimize
&cntrl
imin=1,maxcyc=10000,ncyc=5000,
cut=10.0,ntc=2,ntf=2,ntb=1
/

Heat

Keep protein fixed with weak restraints, hold volume constant

heat
&cntrl
imin=0,irest=0,ntx=1,
ntb=1,cut=10.0,ntr=1
nstlim=100000,dt=0.002,
tempi=0.0,temp0=300.0
ntc=2,ntf=2,ntwx=100,
ntt=3,gamma_ln=2.0,
/
Keep protein fixed with weak restraints
10.0
RES 1 12
END
END

Hold Pressure constant

heat
&cntrl
imin=0,irest=1,ntx=5,
ntb=2,ntp=1,cut=10.0
nstlim=100000,dt=0.002,
temp0=300.0
ntc=2,ntf=2,ntwx=100,
ntt=3,gamma_ln=2.0,
/

Prod

Hold Pressure constant

stage 2 equilibration 50ns 
&cntrl
imin=0,nstlim=25000000,dt=0.002,
irest=1,ntx=5,
ioutfm=1,ntxo=2,ntwv=-1
ntc=2,ntf=2,
ntb=2,ntp=1,
temp0=300.0,
ntpr=5000,ntwx=10000,
cut=10.0,
ntt=3,gamma_ln=2.0,
/

Implicit solvent

Force field FF14SB

Temperature control

ntt=3,gamma_ln=1

RMSD

one dimensional free energy landscape

Trpcage

implicit

rmsd

free energy landscape

trpzip2 start with native state

ntt=1 && igb=1

ntt=3 && igb=1

ntt=1 && igb=8

ntt=3 && igb=8