No residue names shown in the output of mindist -or option

[ka123]

GROMACS version: 2020.2
GROMACS modification: No
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Hi,

I have a question about the command, mindist.
I’m currently running a simulation of the water box containing one protein and one ligand.
I’m studying the interaction between two, and now I’m trying to obtain the information of the name of the each residue pair in contact (especially the name of the residues of the protein in contact with the ligand) and the minimum distance between them.
I used the mindist command with the option -printresname yes. The full command I used is as follows [select protein as the first group, and select ligand as the second group]:

gmx_mpi mindist -s md_0_1.tpr -f md_0_1_noPBC_whole.xtc -od mindist_1_.xvg -on numcont_1.xvg -o atm_pair_1.out -or mindist_res_1.xvg -respertime yes -printresname yes -d 0.6

I expected to see the residue names of the protein in contact in the output file mindist_res_1.xvg, however, I only see the value of the each distance and don’t see any names on the first row. Hence, I don’t quite know which distance value is for which residue.
I attached a part of the image of the output file mindist_res_1.xvg (converted to .csv) below as a reference.

I’m probably missing something out or doing something wrong, but haven’t had a luck of figuring this out by myself.
I appreciate your help in advance.

Best,
Karin

[alevilla]

Hi,

The command -printresname writes the residues names of the first group at the begin of the xvg file. If you open the xvg file with a normal editor (not excel) you should see a line that looks like

\ # LYS0 VAL1 PHE2 GLY3 ARG4 CYS5 GLU6 LEU7 ALA8 A
If you open the file with xmgrace you can see that the first column is read as the time and all the other columns correspond to the minimum distance of each of the residue of group 1 with group 2.
Below a screenshot of output where group 1 is a protein and group 2 solvent

I hope it makes clear.
Alessandra

[ka123]

Hi Alessandra,

Thank you so much for your help! I was totally forgetting about checking the xvg file, thought the output .csv would be exactly the same as .xvg.
Thank you a lot!

Best,
Karin