Fatal Error in Ligand

Hi everyone,
I’m have a some problem when I try to run parameterization using Amber.

here the log file:
------- .R<LIG 391>.A<C 1> and .R<LIG 391>.A<O 2>
FATAL: Atom .R<LIG 391>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 391>.A<O 2> does not have a type.
FATAL: Atom .R<LIG 391>.A<H 3> does not have a type.
Failed to generate parameters
Parameter file was not saved.

I already try to change the atom type but it doesn’t work.


I recognize that this is LEaP output text, and I believe I know what’s the problem.
I see your residue name is LIG, so I have to assume that you are using a non-standard ligand. For those, you have to build topology and charges manually. AmberTools has a program Antechamber you can use for that, check out the hyperlink. The problem you’re experiencing in LEap will be solved once Antechamber creates atom types.

I see this was posted 6 days ago, so I hope you already managed to solve the problem. If not, I hope this helps.

Best regards,