Superimposing same protein from different runs

GROMACS version: 2020.2
GROMACS modification: No

Hi everyone,

I’m running simulations of a protein bound to 3 different ligands. Once they’re done I’d like to superimpose them all so I can carry out some PCA and other analyses.

I was thinking of using trjconv -fit but I’m not sure if this will work with three different index/tpr files. The protein atoms all correspond to each other, but the ligands have a different number of atoms so they won’t match. If it makes it any easier, I’m not interested in any of the membrane or solvent molecules in the trajectories, just the protein and ligand.

Can anyone advise?

You can do all the protein-specific analysis using .tpr and trajectory files that contain only the protein (gmx convert-tpr to generate the subset .tpr file and gmx trjconv for the trajectories). That will work for superimposition, PCA, etc.

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I was hoping I could keep the ligands so I could later build a volumetric map of the extent of pocket occupation, but your solution works for the PCA nonetheless, thanks!

Just wondering, after running gmx mk_angndx the resulting index file has a number of groups, with the most populated one called [ Phi=0.0_3_0.84 ]. When running gmx angle it asks for a group selection, I’m guessing I go for the group with the most elements, but what are all these groups in the first place? I couldn’t find any detail in the manual about them.

UPDATE: gmx angle hangs after “Found points in the range from 0 to 359 (max 360)” when the [ Phi=0.0_3_0.84 ] group, with 1152 elements, is selected. It works with all the other groups. I’ve tried letting it run for a longer time (more than proportional to the number of elements in other groups) but it doesn’t stop hanging.

The other strange thing is whether I specify -nohyd or not, the resulting index files are identical. Yet I thought this was on by default?