Dear Amber users,
I am using a a subunit of a protein can form a homodimer or heterodimer. I
want to characterize the flexibility of its N-terminal and C-terminal
domains.
My problem is The RMSD during equilibration phase increases approx.
linearly, which may indicate unfolding of the protein . I ran equilibration
for 1 ns. Please, any one has sugestions.
The potocol of heating is
&cntrl
imin = 0, irest = 0,
ntb = 1, ntx = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi= 0.0, temp0 = 298.0,
ntt = 3, gamma_ln = 1.0, ntp = 0,
nstlim = 100000, dt = 0.002,
ntpr = 500, ntwr = 500,
ntwx = 500,
/
Keep solute fixed with weak restraint
500.0
RES 1 181
END
END
The protocol for equilibration is
&cntrl
imin = 0, irest = 1,
ntb = 2, ntx = 5,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
temp0 = 298.0,
ntt = 3, gamma_ln = 1.0, ntp = 1,
nstlim = 100000, dt = 0.002,
ntpr = 500, ntwr = 500,
ntwx = 500,
&END
All the best
Ibrahim
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Received on Wed Sep 10 2014 - 13:30:04 PDT
