Dear Carlos,
Thanks for the email.
The protein-peptide complex which I am trying to simulate has 225 residues
and the peptide is 10 residues long. The peptide interacts with the protein
through 3 hydrogen bonds at one end. The residues at the other end of the
peptide are free (non interacting).
First, I ran 2000 cycles of minimization on the complex after creating the
.prmtop file form tleap.
Next, I equilibrated the complex at constant volume, temperature and then
pressure.
Then i collected production run for 15ns (1500 frames)
After the run, I calculated the r.m.s.d. of coordinates generated using
ptraj:
trajin abc.mdcrd 1 1500 1
reference ref.pdb
rms reference out rmsd.dat .CA, C, N, O
go
r.m.s.d of the coordinates generated during the simulation, fluctuate a
great deal and then jump sharply after ~10ns and progressively keeps
rising.
Find attached the r.m.s.d. graph over 15ns (1500 frames).
I looked at the trajectory. Over these 15ns the peptide fluctuates such that
at one point (after about 10ns) the distance between the CA of a peptide
residue (which makes hydrogen bond with the protein) is ~10 A with the
reference. Please help!
Thanks,
Po
On Thu, Aug 4, 2011 at 4:44 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> You don't tell us very much. For example which atoms are used in rmsd? It
> is
> the part that you said is expected to fluctuate? Also, what did you do to
> calculate rmsd? Did you use any sort of periodic imaging? Have you
> visualized this trajectory to see what is happening? My rule is to always
> look at your primary data (coordinates, through a viz program) and the do
> numerical analysis to quantify what you see in the data. Never, ever skip
> the step of actually looking at the molecule.
> On Aug 4, 2011 3:00 AM, "Xiao Chen" <chen.xiao.po.gmail.com> wrote:
> > Dear All,
> >
> > I am trying to simulate a protein-peptide complex. the peptide is ~10
> > residues out of which 3 at one end are interacting with the protein. The
> > other end of the peptide is free to fluctuate. I ran a simulation of 10ns
> > and it was observed that the r.m.s.d of the coordinates generated during
> the
> > simulation becomes very high after ~2ns and progressively keeps rising
> after
> > that. This could indicate that something is not okay with the simulation.
> > Can you suggest what I can alter to stabilize the simulation?
> >
> > Thanks,
> >
> > Po
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Received on Fri Aug 05 2011 - 03:30:02 PDT
