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

Sarath Chandra sarathchandradantu at gmail.com
Fri Apr 22 11:50:58 CEST 2016

You can make an index group with both protein+ligand using make_ndx command
and use the index file from make_ndx to run the rmsd analysis



Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India

On 22 April 2016 at 15:16, 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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