Can you tell us more about the initial structure? Where did it come from?
Is there anything unusual about your setup?
On Sep 10, 2014 4:22 PM, "Ibrahim Said" <saidibrahim569.gmail.com> wrote:
> 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 Thu Sep 11 2014 - 06:00:02 PDT
