Can anyone help me how to make index file in gromacs for protein-ligand system ?

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Qingwei Gao Popular answer

use the command gmx make_ndx

Qingwei Gao

Shivani Gupta

Thankyou , i tried its working

Anwesh Pandey

follow this:

Code GROMACS (CHARMM)

Code GROMACS (AMBER)

thankyou anwesh for the help

i am gonna try this.

is the script that you have shared, needs to be run by direct submission or it is a perl script ?

Shivani Gupta direct submission

Noeman Ardalan

using gmx make_ndx

Rajlaxmi Saha

Refer to this website to make an index file using GROMACS http://manual.gromacs.org/archive/5.0.4/programs/gmx-make_ndx.html