Dear AMBER users,
I am currently on a project where the objective is to design a protein model (1304 amino acids).
There are 3 long chains present on the protein model. One of the shorter chains has finally folded and now left with 2 long chains.
Restrains were applied on the model letting only 1 long chain to fold at a time.
AMBER version 2011 was used throughout the simulation process.
The parameter used was:
imin = 0,
ntb = 0,
igb = 0,
cut = 10.0,
ntr = 1,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 100000,
dt = 0.001,
ntpr = 100,
ntwx = 100,
ntwr = 100
/
I wonder is there a better/quicker way in folding the long chains? As I would need the final model as soon as possible.
Thanks in advance.
Best regards,
Li Zhe
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Received on Tue Jan 17 2017 - 19:00:02 PST
