[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


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
> --
> 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.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>


More information about the gromacs.org_gmx-users mailing list