Dear amber users,
I am trying to refine docked pose simulated annealing. However, after the simulated annealing the structure of protein is completely lost. Can someone guide me?
I am following protocol:
# Heating 20ps
&cntrl
imin = 0,
irest = 0,
ntc=1, ntf=1, ntx = 1,
ntwx=1000, ntpr = 1000, ntwe=1000, ntwr = 10000,
ntb = 0, cut = 999.0,
igb = 5, saltcon=0.2,
nstlim = 40000, dt = 0.0005,
ig=-1,
ntt = 3,
gamma_ln=50.0,
tempi=0.0,
temp0=300.0,
nmropt=1,
restraintmask= ':1-386',
restraint_wt=10,
/
&ewald
eedmeth=5,
/
&wt type='TEMP0', istep1=0, istep2=39000, value1=0.0, value2=300.0, /
&wt type='TEMP0', istep1=39001, istep2=40000, value1=300.0, value2=300.0, /
&wt type='END'
/
# equlibirate 80ps
&cntrl
imin = 0,
irest = 1, ntx=5,
ntc=1, ntf=1,
igb = 5, saltcon=0.2,
ntwx=1000, ntpr = 1000, ntwe=1000, ntwr = 1000,
ntb = 0, cut = 999.0,
nstlim = 80000, dt = 0.001,
ntt = 3, gamma_ln=5,
temp0=300,
ig=-1,
restraintmask= ':1-385.CA,C,N & :386',
restraint_wt=10,
/
&ewald
eedmeth=5,
/
#simulated annealing and equilibration protocol, 300ps
&cntrl
ntx=5, irest=1,
imin = 0,
ntc = 1, ntf=1,
ntb=0, cut = 999.0,
igb = 5, saltcon=0.2,
nstlim=600000, dt= 0.0005,
ntt=3, gamma_ln=2,
ig=-1,
temp0=300,
ntwx=1000, ntpr = 1000, ntwe=1000, ntwr = 1000,
nmropt = 1,
restraintmask= ':1-385.CA,C,N & :386',
restraint_wt=10,
/
&ewald
eedmeth=5,
/
#heating followed by equilibration
&wt type='TEMP0', istep1=0, istep2=50000, value1=300.0, value2=400.0, /
&wt type='TEMP0', istep1=50001, istep2=100000, value1=400.0, value2=400.0, /
&wt type='TEMP0', istep1=100001, istep2=150000, value1=400.0, value2=500.0, /
&wt type='TEMP0', istep1=150001, istep2=200000, value1=500.0, value2=500.0, /
&wt type='TEMP0', istep1=200001, istep2=250000, value1=500.0, value2=600.0, /
&wt type='TEMP0', istep1=250001, istep2=300000, value1=600.0, value2=600.0, /
&wt type='TEMP0', istep1=300001, istep2=350000, value1=600.0, value2=500.0, /
&wt type='TEMP0', istep1=350001, istep2=400000, value1=500.0, value2=500.0, /
&wt type='TEMP0', istep1=400001, istep2=450000, value1=500.0, value2=400.0, /
&wt type='TEMP0', istep1=450001, istep2=500000, value1=400.0, value2=400.0, /
&wt type='TEMP0', istep1=500001, istep2=550000, value1=400.0, value2=300.0, /
&wt type='TEMP0', istep1=550001, istep2=600000, value1=300.0, value2=300.0, /
&wt type='END'
/
#120ps cooling
&cntrl
imin = 0, irest = 1, ntx=5,
ntc=1, ntf=1,
igb = 5, saltcon=0.2,
ntwx=1200, ntpr = 1000, ntwe=1000, ntwr = 1000,
ntb = 0, cut = 999.0,
nstlim = 100000, dt = 0.001,
ntt = 3, gamma_ln=1.0,
temp0=300,
nmropt=1,
ig=-1,
restraintmask= ':1-385.CA,C,N & :386',
restraint_wt=10,
/
&ewald
eedmeth=5,
/
&wt type='TEMP0', istep1=0, istep2=10000, value1=300.0, value2=250.0, /
&wt type='TEMP0', istep1=10001, istep2=20000, value1=250.0, value2=250.0, /
&wt type='TEMP0', istep1=20001, istep2=30000, value1=250.0, value2=200.0, /
&wt type='TEMP0', istep1=30001, istep2=40000, value1=200.0, value2=200.0, /
&wt type='TEMP0', istep1=40001, istep2=50000, value1=200.0, value2=150.0, /
&wt type='TEMP0', istep1=50001, istep2=60000, value1=150.0, value2=150.0, /
&wt type='TEMP0', istep1=60001, istep2=70000, value1=150.0, value2=100.0, /
&wt type='TEMP0', istep1=70001, istep2=80000, value1=100.0, value2=100.0, /
&wt type='TEMP0', istep1=80001, istep2=90000, value1=100.0, value2=50.0, /
&wt type='TEMP0', istep1=90001, istep2=100000, value1=50.0, value2=50.0, /
&wt type='TEMP0', istep1=100001,istep2=110000, value1=50.0, value2=0.0, /
&wt type='TEMP0', istep1=110001,istep2=120000, value1=0.0, value2=0.0, /
&wt type='END'
/
# slow cooling 80ps
&cntrl
imin = 0, irest = 1, ntx=5,
ntc=1, ntf=1,
igb = 5, saltcon=0.2,
ntpr=100, ntwx=1000,
ntb = 0, cut = 999.0,
nstlim = 80000,
dt = 0.001,
ntt = 3, gamma_ln=1000.0,
temp0=0.0,
restraintmask= ':1-386.CA,C,N',
restraint_wt=10,
/
&ewald
eedmeth=5,
/
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543, Republic of Singapore: sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; Phone +6582969643; http://www.linkedin.com/in/imsharmanitin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 25 2014 - 12:00:02 PDT
