GROMACS version: 2020.4
GROMACS modification: No
Hi, when I want to convert my .xtc trajectories to PDB I use “gmx trjconv -s .tpr -f .xtc -dt -o .pdb”.
Is there any way to do this to include both protein and ligand rather than one or the other?
This is done via either the default groups generated when you run the script (a list of options appears when you run the command, asking what you want to include in the output). If the combination you want isn’t in that default then, then you make your own index file (
gmx make_ndx -f .tpr -o index.ndx) and pass that to the command (
gmx trjconv -s .tpr -f .xtc -n index.ndx -o .pdb) and select the appropriate group you generated.