Thanks Carlos, I am redoing the calculation.
On Mon, Oct 30, 2017 at 1:22 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> yes, it affects your trajectory and the results will differ from those
> where the restraints were applied to different atoms. Will it make your
> trajectory "wrong"? It's very hard to say- but in any case, you would need
> to clearly explain this mistake in any publication of the data, so I would
> probably redo the calculation with the correct atom mask unless it's
> impossible to do so.
>
> On Mon, Oct 30, 2017 at 8:14 AM, sangita kachhap <nckachap.cyf-kr.edu.pl>
> wrote:
>
> > Hi everyone,
> >
> > I am doing MD simulation of protein-ligand complex. I was needed to apply
> > restraint_wt on protein backbone and ligand heavy atoms only during
> > minimization (50 kcal/mol −Å) and heating (5 kcal/mol −Å) but by mistake
> I
> > applied it to all the atoms of ligand and some of the TIP3P water
> molecules
> > along with protein backbone. I have done NPT equilibration for 2.4 ns
> > before production run.
> >
> > I have a question, will it affect the MD calculations from the scenario
> > when I don't have to apply restraint on ligand's hydrogen atoms and some
> of
> > the TIP3P water molecules?
> >
> > Thanks
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Received on Mon Oct 30 2017 - 06:30:02 PDT
