[gmx-users] RMSD calculation of protein-ligand complex

[Catarina A. Carvalheda dos Santos]

Hi,

You can create a group with the protein and the ligand using the make_ndx
tool. Then you can use the created index file as input for your rmsd
calculation.

Cheers,
On 22 Apr 2016 10:47, "Aswathy soman" <aswathyneeharika at gmail.com> wrote:

> Hi,
> I have done a 100 ns simulation of protein-ligand complex. I was wondering
> is it possible to calculate RMSD of the entire protein-ligand complex. How
> to select the complex as such during the calculation of RMSD because there
> is no group as protein+ligand. Thanking you in advance
>
> Regards,
> Aswathy
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