Why the mutation can not be executed thoroughly?

[JonasLi-19]

when I use pyrosetta to convert protein amino acid, there is some amino acid keep their original state, some others converted as I commanded.

The function I used is MutateResidue(). As the picture below, the LEU is a converted AA from ASN, but there is still one ASN cannot to be concerted into LEU.

[roccomoretti]

It's hard to say without knowing which residue is unable to be mutated, but often the issue is related to the patch state of the residue in question, particularly patches which change the connectivity of the residue.

I would recommend doing a pose.residue(seqpos).name() to see the full name of the residue type at the position which can't change. If it's something like "ASN:CTermProteinFull", the part after the colon is the patch name. When you use MutateResidue, you may have to match the patch state of the residue you're mutating things to (e.g. "LEU:CTermProteinFull").

[Dadiao-shuai]

I want to know if the partial charge be calculated after using amino acid mutation, should I do more work before using the mutated protein for AutoDock4 docking?