Dear AMBER users,
I want to model the folding of the C-terminus of a protein. The protein consists of 120 residues. For the last 11 residues, there is no structure available. My aim is to model the missing 11 residues using AMBER 12. I have done the initial steps (minimization, heating, equilibration). Now I'm planing to carry out the production. Here is the input file:
&cntrl
imin=0, irest=1, ntx=5,
nstlim=1200000, dt=0.002,
ntc=2, ntf=2, igb=8,
cut=10, ntb=0, ntp=0, taup=2.0,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=2.0,
temp0=300.0
/
Hold PROTEIN fixed
5.0
RES 1 94
END
END
1) I hope there may be similar work done before using AMBER, I will be thankful to you, if you could kindly enlighten me some similar work.
It will be grateful for me, if someone of you kindly give me latest publications, which explain the mechanism as well as production and analysis in detail.
2) For the publication, what may be the criteria to judge the model and how many cycles I need to run to get the reasonable model?
Thank you in advance!
Aylin
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Received on Tue Aug 13 2013 - 00:00:03 PDT
