Protein-Ligand Complex Analysis FIRST FRAME EXTRACTION

User discussions
1

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:)

Thanks:)
Joel

2

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.

3

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.

4

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.

Best,
Joel