Convert protein & ligand .xtc to same PDB file

User discussions
1

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?
Thanks

2

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.

1 Like
3

Hi @Dr_DBW @jalemkul @hess @alevilla

The command gmx trjconv -s .tpr -f .xtc -n index.ndx -o .pdb gives a PDB without chain names, in contrast to the original PDB used for molecular dynamics (MD) simulation, which included chain information. Is there anyway to retain the original chain names in the PDB file extracted from the xtc and tpr files?

Thanks