Alternatives for GROMACS output files

[fidelrmz]

Hi!
I have recently installed PyContact to analyze some trajectories performed with GROMACS. However, I am aware neither topology nor trajectory output files obtained with GROMACS have any defined segment ID (segid) to use for selection in PyContact (already checked by MDAnalysis). Tried transforming .gro to .pdb files in order to attempt using chains ID but eventually failed. After some reading I found VMD is a possible solution through psfgen but also failed due to an 'apparently not so uncommon' error while running and which has also been reported in VMD's mailing-list for a long time. Anyway, I was wondering if maybe there is any other alternative for selection data to evaluate GROMACS trajectory files with PyContact since looks like the precise tool for what I need right now. Thank you in advance!

[maxscheurer]

Hi,
yeah this is a common problem I've encountered as well 😦
Except for making use of the existing MDAnalysis selection language, I have no other alternative in mind.

About the conversion: maybe it could work with parmed?

I think in the long run it would be best to be able to load pure pdb trajectories into PyContact, but I won't have time to implement that in the near future...