Thank you all
My protein is a pdb file and it has x-ray coordinates and its resolution is
2.10 A. The forcefield is ff12SB and TIP3P water model is the solvent. I
hope I can find a help. I will start to change the forcefield may it is the
cause as I read in internet.
Ibrahim
On Thu, Sep 11, 2014 at 2:43 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> >
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Received on Thu Sep 11 2014 - 08:00:03 PDT
