Re: [AMBER] Parametarization error

From: Bill Ross <>
Date: Wed, 17 Oct 2018 21:45:59 -0700

> FATAL: Atom .R<UNK 468>.A<C36 12> does not have a type.

Looks like you didn't create a template for your residue? See tutorials
(biotin might be good). Res/atom names must match between template and pdb.

> Could not find bond parameter for: Cg -

> Could not find angle parameter: Cg - Cg -

It looks like a blank-space atom type might have slipped through Interpol's net. Maybe if you fix the residue template, you will be able to fix that from the experience.


On 10/17/18 9:34 PM, senal dinuka wrote:
> I have been trying to generate prmtop and inpcrd files for the below
> mentioned receptor/ligand complex. The ligand is a TS structure hence the
> weird bond lengths. I was told to use GLYCAM for the sugar portion and
> separate frcmod for the cyanogenic part of the ligand since GLYCAM doesnt
> offer parameters for the later. Hence I generated a l1.frcmod with bcc
> charge scheme through antechamber and parmchk modules with default options.
> frcmod seem to be lack in bond and angle properties. And thus the leap
> results in error I assumed. I appreciate your guidance regarding the matter.
> Thank you
> P.S I have attached the complex, ligand as well as frcmod and leap script I
> used
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Received on Wed Oct 17 2018 - 22:00:03 PDT
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