Re: [AMBER] Parametarization error

From: David Case <>
Date: Thu, 18 Oct 2018 18:09:55 +0000

On Thu, Oct 18, 2018, 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.

You have a residue named "UNK" (which usually stands for "unknown").
You will need to create a unit file for that (usually in .mol2 format).
See tutorials about creating Amber libraries for organic ligands (e.g.
the "sustiva" tutorial) for help in getting started.

...good luck....dac

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Received on Thu Oct 18 2018 - 11:30:03 PDT
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