<< Trajectories from xTB package >>

[icamps]

Hello,

I am using Pycontact for the first time.

My molecular dynamic calculation where done with the xTB software. The trajectory format is just a XYZ-like file with each frame in sequence. Using VMD, I created a multimodel PDB: also each frame is in sequence.

Is it possible to use those results with Pycontact? I tried to load the files but I got the error:
Error while loading data: Probably you specified an atom selection with 0 atoms or invalid input files

Is it possible to use Pycontact work with xTB?

Regards,

Camps

[moraisb]

I had a similar issue. It seems that Pycontact is optimized for use of psf topology files and dcd trajectory files. After a lot of pain and misery, I found a simple solution for converting Amber .top and .crd files to .psf and .dcd which may also work for your case. To get the dcd file I used VMD's molecule file browser to open my .top and .crd files then I saved the coordinates as a dcd. The process is explained in this video: https://www.youtube.com/watch?v=fR4wSdKL0sI . I got the .psf by installing the program Parmed and using it in a Jupyter notebook. This was pretty straightforward if you use the provided examples as a guide. You will then have to use a text editor to manually change the segids which are "SYS" by default. I used Textedit in Mac to do a vertical selection of the parts I wanted to rename, then used find and replace to replace "SYS" in that selection block with my preferred segid and saved. You could probably use Parmed to translate your trajectory file as well but I made my dcd file before learning about Parmed so that wasn't necessary fro me. After doing all that you should be good to go.

[icamps]

Thanks @moraisb for the suggestions.