[gmx-users] Protein-Ligand Interaction calculation

[Александр Лашков]

You can rebuild index file using gmx make_ndx gromacs util.
Alex

пн, 17 февр. 2020 г. в 15:19, Peter Mawanga <peter.mawanga.lagos at gmail.com>:

> Hello everyone
>
> I used the CHARMM-GUI Membrane Builder to build a bilayer around my
> protein-ligand complex.
>
> However, unfortunately the ligand was not mentioned separately in the index
> (.ndx) file although it was mentioned in the topology (.top) file. Hence I
> am not able to calculate the energy between the protein and ligand using
> the energy (.edr) file.
>
> Please let me know if there is any workaround for this. It would be
> difficult to repeat the simulations again.
>
>
> --
> Cheers
> Peter
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