mol2 file generation

[haroldgrosjean]

Hello,

I am very interested in using your (amazing) tool to carry out advanced contact analysis of my protein-ligand simulations.

Could you recommend a way to convert the first frame (.gro file) of my gromacs trajectory (.xtc file) into a suitable mol2 file?

Many thank

Harold

[marcvdijk]

Dear Harold, Thank you for considering MDInteract for your research. At the moment I am unable to answer your question in detail for at least another week but I will as soon as I can. Best regards, Marc van Dijk

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Op 25 sep. 2020 om 14:15 heeft haroldgrosjean ***@***.***> het volgende geschreven: Hello, I am very interested in using your (amazing) tool to carry out advanced contact analysis of my protein-ligand simulations. Could you recommend a way to convert the first frame (.gro file) of my gromacs trajectory (.xtc file) into a suitable mol2 file? Many thank Harold — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[marcvdijk]

Dear Harold,

Returning to your question. There are no conversion methods to mol2 files part of the package yet.
The strategy I follow is to extract the first frame as PDB file and then using OpenBabel to convert it to mol2.
You can use the underlying MDTraj Topology object to select the first frame and save it as PDB (see MDTraj docs) or use the Gromacs tools to do the same.

Regards,

Marc