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 - 05:30:04 PDT
