ERROR: [NotSupportedInScoringError] Residue A.SER.1 or atom HT1 not supported. DFIRE only supports standard aminoacids without hydrogens. about lightdock HOT 9 CLOSED

A quick list of all of them:

lightdock3.py --listscoring
Available scoring functions are:  tobi, sd, dfire, fastdfire, cpydock, template, vdw, pisa, ddna, dna, dfire2, mj3h, sipper

Each of them in the list above have an independent folder at: https://github.com/lightdock/lightdock/tree/master/lightdock/scoring

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Hi @o5728492 , remove all hydrogens and HETATM from your input structures, DFIRE scoring function only supports standard residues. Also make sure there are no residues with missing backbone atoms if you enable ANM.

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Hi @o5728492 , remove all hydrogens and HETATM from your input structures, DFIRE scoring function only supports standard residues. Also make sure there are no residues with missing backbone atoms if you enable ANM.

Defining HETATM residues is supported here; However, all HETATM needs to be deleted when errors are reported. Isn't this a conflict？

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FAQs for lightdock

Lightdock supports some different scoring functions,the default DFIRE doesn't support HETATM restraints,others might support.

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One thing is LightDock, the other thing is the scoring function. You can have HETATM entries in your PDB files and perform the setup without running into issues (nothing new here as you can see in the issue above) and even define those as residue restraints (the new addition in the release you are referring to). However, for the simulation all HETATM need to be parametrised within the scoring function of your choice. This last consideration is, however, up to the user. We can provide some guidelines if you wish.

from lightdock.

FAQs for lightdock

Lightdock supports some different scoring functions,the default DFIRE doesn't support HETATM restraints,others might support.

What scoring functions LightDock has, and what others support？

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One thing is LightDock, the other thing is the scoring function. You can have HETATM entries in your PDB files and perform the setup without running into issues (nothing new here as you can see in the issue above) and even define those as residue restraints (the new addition in the release you are referring to). However, for the simulation all HETATM need to be parametrised within the scoring function of your choice. This last consideration is, however, up to the user. We can provide some guidelines if you wish.

Thank you. In addition, please confirm whether LightDock protein-protein docking is flexible or rigid？

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You will find more information on the tutorials section, but this is the most relevant part to answer your question about flexibility:

It is capable of modeling protein-protein, protein-peptide and protein-DNA interactions in rigid-body fashion or modeling backbone flexibility using Anisotropic Network Model (ANM). If ANM mode is activated, LightDock calculates the Ca-Ca ANM model using the awesome ProDy Python library. By default, the first 10 non-trivial normal modes are calculated for both receptor and ligand (in every residue backbone and further extended to the side-chains)

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Again, take the time to read our tutorials and publications since you might find useful insights to your queries. Why do we then take the time to write them? :)

Questions != issues

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