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

[Sarath Chandra]

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

Regards,

Sarath

-- 
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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>