[gmx-users] INDEX

Erik Marklund erik.marklund at kemi.uu.se
Mon Feb 6 13:37:48 CET 2017

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv -n your_index_file.ndx …

Kind regards,
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 6 Feb 2017, at 13:06, Subashini .K <subashinik at hotmail.com<mailto:subashinik at hotmail.com>> wrote:

Hi gromacs users,

I want to visualize the results of simulations using the command

gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb

Wish to see Protein and ligand simulations together in the pdb file.

But, when the command is given, we can either select protein group or ligand group

Before this was done,

The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt

However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in the movie.pdb file.

What to do?

Can someone help?



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