If you're using torsional restraints, then I think looking at the torsional
values is better than rmsd. You may have small deviations in torsions (10
degrees,with no penalty as you defined) that give large rmsd values car
away from that torsion. It's also not clear if the reference structure
matches the restraints, or if the rmsd comparison mask is fully defined by
the restraints.
In general I would only expect the rmsd to remain low if you used
positional restraints, or an rmsd based restraint. It's difficult to know
if your structure should be stable under these conditions. It depends on
how it was equilibrated, the force field used, whether the older igb=5 gb
models is sufficient here, the intrinsic Born radii set, and many other
things. I guess my point is that if these things aren't ideal, then the
structure may deviate and torsion restraints are not always sufficient to
ensure a low rmsd. You may need to look carefully at the restraint
violations, and visually inspect the structure trajectory to see where the
rmsd deviations are most significant.
On Tue, Sep 17, 2019, 9:15 AM Amit Kumar <ak543714.gmail.com> wrote:
> It was backbone torsional restraint (phi, psi angles were restrained) of
> 2.0 kcal/mol *.* rad, with lowerbound -10 degree from the dihedral angles
> of protein in pdb and with upperbound +10 degree. The NMR violation energy
> was generally in the range of 10-14kcal/mol but at the deflection point
> (where RMSD increased suddenly) it was nearly 17kcal/mol and after that it
> increased upto 22 kcal/mol.
>
> The Input Script:
> &cntrl
> imin=0,
> irest=1,
> ntx=5,
> ntpr=2000,
> ntp = 0, ntwx=100, nstlim=2500000,
> dt=0.002, ntt=3,
> temp0=298, gamma_ln=1.0, ig=-1,
> ntc=2, ntf=2, cut=999, rgbmax = 30.0,
> ntb=0, igb=5, ioutfm=1, nmropt=1,
> /
> &wt TYPE='END' /
>
> DISANG = tor.out
>
> On Tue, Sep 17, 2019 at 4:28 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > What kind of restraints did you use, and how strong? How high is the
> > penalty energy in the mdout file?
> >
> > On Tue, Sep 17, 2019, 5:15 AM Amit Kumar <ak543714.gmail.com> wrote:
> >
> > > I am really very sorry sir, I miswrote the question.
> > > I found the RMSD value of the restrained system higher than the
> > > unrestrained system, which is very unusual. I am also attaching the
> > > result.
> > >
> > > On Mon, Sep 16, 2019 at 6:57 PM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > Yes this is very sensible. I would expect that the restraints would
> > keep
> > > > the structure closer to the initial model (if that's what you use as
> > the
> > > > reference for rmsd), leading to lower rmsd with the restrained
> > > trajectory.
> > > >
> > > > On Mon, Sep 16, 2019, 9:20 AM Amit Kumar <ak543714.gmail.com> wrote:
> > > >
> > > > > Dear Amber users,
> > > > > I ran a simulation of a fibrillar protein for few nanosecond (with
> > and
> > > > > without torsional restraint) using Amber16. I used implicit solvent
> > > > (igb=5)
> > > > > results when analysed in terms of RMSD, the RMSD value of the
> > > > unrestrained
> > > > > system was higher than the RMSD value of the restrained system. Is
> it
> > > > > possible? Can you explain the phenomenon?
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Received on Tue Sep 17 2019 - 09:00:02 PDT
