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 - 06:30:02 PDT
