Re: [AMBER] Equilibration phase and RMSD

From: Ibrahim Said <saidibrahim569.gmail.com>
Date: Thu, 11 Sep 2014 21:18:17 +0200

The protein is a structural protein involved in the formation of dimer or
tetramer or octamer complexes with the protein or other proteins. For
heating stage (200 ps), the RMSD became 20 A and then after equilibrtion
the RMSD increased to 50 A. I calculated the RMSD using the minimized
structure as the reference. please find the RMSD plot as attached file.


On Thu, Sep 11, 2014 at 5:05 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> thanks, it wasn't clear since you said it could form a homodimer or
> heterodimer. if you're simulating the entire system that is in the pdb file
> it should be reasonably stable, at least for a while. Of course it needs
> careful equilibration. We normally do this in many steps. when you say that
> the RMSD increases linearly, can you tell us what the input file is for the
> step when it increases, and what the values of the RMSD are during that
> step?
>
> On Thu, Sep 11, 2014 at 10:56 AM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
>
> > 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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Received on Thu Sep 11 2014 - 12:30:02 PDT
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