Protein-Ligand Complex Analysis FIRST FRAME EXTRACTION

GROMACS version: 2020.3
GROMACS modification: Yes/No
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Hello for the above topic my understanding is that via the commands:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact

gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0

my output start.pdb should contain the ligand, solvent and ion coordinates to match the tutorials exhibited below visualization via VMD, however, my output start.pdb only contains protein coordinates (my md_0_10.gro contains protein-ligand-sol-ion coordinates). Any clarification would be helpful:)


I can only imagine two places where you might have gotten rid of the water (if you double-checked the end of start.pdb in the terminal to make really sure it didn’t contain the lines for water):

  1. You might have chosen to only write the protein to the compressed trajectory by using the xtc-grps option in the mdp file.

  2. You selected “1” for the interactive option when asked (at either invocation) by gmx trjconv about what group to write to the output.

You might have .mdp output settings to only give you the protein coordinates in output to save disk space. Changing
compressed-x-grps will change that to give you more output on the trajectory.

Hello Sir Lindhal and thank you for your kind update, yes I carelessly selected 1 initially for the later command out of habit via the former command selection.