Res type not allowed message!?

[biotech70]

My peptide has 8 residues and does not accept any residual change when I submitted complex of it with the receptor to Kstar algorithm. What is the cause of this error Res type Ala not allowed at position B2, can incorrect preparation of the input structure cause this?

[cuchaz]

Hmm... looks like that might be a bug in Osprey. Looking at the commit history, it looks like multiple developers have tried to make residue types case-insensitive, but the results are a bit inconsistent. I'll see if I can fix it.

For now, I think you can work around the bug by using all uppercase letters for your residue types. eg, try ALA everywhere instead of Ala.

[biotech70]

Thank you, your recommended method answered. But the question that has been on my mind is, do I have simultaneous mutations in OSPREY or mutations applied singularly?

[cuchaz]

K* has a setting for that, try this one: https://github.com/donaldlab/OSPREY3/blob/main/src/main/python/osprey/__init__.py#L1066 https://github.com/donaldlab/OSPREY3/blob/main/src/main/java/edu/duke/cs/osprey/kstar/KStar.java#L93

[biotech70]

thanks dear Jeff for your cooperation and accountability. i used from comets but unfortunately the speed this algorithm is very slow, indeed for below input after two hours computation not completed, while 8 CPU core and 1 GPU was used for processing.