Hi,
I'm performing an NMR refinement and would like to use a minimized structure and perform multiple refinements with ligand-protein NOEs. I'm trying to use the same protein structure each time, and just use a different random number seed to get an ensemble of results. I'm using AMBER 7, and I've set ig=different random numbers, but the calculation starts every time from the input coordinates at time 0.0 ps. Can someone help me figure out how to change this?
Below is my input file:
Thanks in advance!
# 20 ps Simulated Annealing protocol
&cntrl
nstlim=20000, ntt=0,
scee=1.2, ntx=1
ntpr=500, pencut=1.0,
ipnlty=1, nmropt=1,
vlimit=10, ibelly=1
ntb=0, ig=209858, tempi=10.
igb=0,
&end
#
#Simulated annealing protocol
# from steps 0 to 5000 : raise target temperature 10-400K
# from steps 5000 to 10000: leave at 400K
# from steps 10000 to 40000 : re-cool to low temperatures
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=600.,value2=600., &end
&wt type='TEMP0', istep1=5001,istep2=18000,value1=600.,value2=100., &end
&wt type='TEMP0', istep1=18001,istep2=20000,value1=0.0,value2=0.0, &end
#
#Strength of temperature coupling
#
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,value2=0.4, &end
&wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,value2=4.0, &end
&wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,value2=1.0, &end
&wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,value2=0.05, &end
#Restraint control - ramp up restraints over the first 3000 steps
&wt type='REST', istep1=0,istep2=3000,value1=0.1,value2=1.0, &end
&wt type='REST', istep1=3001,istep2=20000,value1=1.0,value2=1.0, &end
&wt type='END', &end
LISTOUT=POUT
DISANG=RST
Group Input for Ligand
1.0
SEARCH
RES 126
END
Group Input for Protein N-terminus:
1.0
SEARCH
RES 1 10
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 14
RES 96
RES 93
RES 50
RES 104
RES 54
RES 57
RES 100
RES 103
RES 86
RES 34
RES 55
END
END
Thanks,
Brad
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Received on Wed Oct 17 2012 - 10:30:02 PDT
