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maxscheurer / pycontact

Analysis of non-covalent interactions in MD trajectories
https://pycontact.github.io/
GNU General Public License v3.0
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Error loading gromacs output file #76

Closed ErikZhang-9762 closed 3 years ago

ErikZhang-9762 commented 3 years ago

Hi, First of all, thank you for developing the program. It looks great! When I used it to load the gromacs file I had some problems, The error message is as follows Error while loading data: Probably you specified an atom selection with 0 atoms or invalid input files.

Here are my inputs Topology ： topol.top Trajectory: md.tpr / md.xtc selection1: segid seg_0_Protein_chain_A selection2: segid seg_1_A60V #A60V is a small organic molecule

I don't know what the mistake is. I really appreciate any help you can provide.

maxscheurer commented 3 years ago

Hi,

please try md.tpr as "topology" file and md.xtc as "trajectory" file, I think that's how MDAnalysis expects the files. Also, you could try to first load both files as an MDAnalysis Universe in a python script Link with

u = mda.Universe("md.tpr", "md.xtc")

and then try out your selections.

ErikZhang-9762 commented 3 years ago

Thanks, it worked for me.