Inniag

As explained by @philbiggin, the issue is that libgromacs has API-breaking changes between the major versions of Gromacs releases and CHAP has not yet been updated to keep up with...

Which version of Gromacs are you using?

Compile against Gromacs 2018. Due to some API breaks in libgromacs 2018, CHAP is not yet compatible with the newer versions of Gromacs.

Hi Christian, are you sure the position you specified lies within then protein? CHAP uses nanometers as units of distance, as is the standard for Gromacs, but many other tools...

Have you tried visualising the pore it finds in e.g. VMD or PyMol? Might give some indication where it goes wrong. From your description, it sounds to me like CHAP...

The pathway finding uses simulated annealing, which is _not_ deterministic in principle. However, you can fix the random seed, in which case results should be reproducible for identical input. Take...

I have not seen this issue before. I suspect it comes from you using CHAP in a way we did not have in mind when writing it. Also, does this...

You would have to write your own Python/R/Matlab code to average the profiles from the trajectory chunks. For confidence intervals, you'd need to decide on how to propagate errors. For...

I can think of two reasons for why hydrophobicity is not computed properly: - Your pore does not consist of amino acids and there is not hydrophobicity information available in...

The error above suggests that Chap can not interpolate the hydrophobicity values at the individual residue positions into a continuous profile. The reason for this is hard to diagnose, it...