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

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Fri Apr 22 11:50:57 CEST 2016


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

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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