GROMACS version: 2020.2
GROMACS modification: No
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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.