Re: [AMBER] restraint_wt applied to wrong atoms

From: Carlos Simmerling <>
Date: Mon, 30 Oct 2017 08:22:20 -0400

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 <>

> 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
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