Re: [AMBER] Parametarization error

From: senal dinuka <>
Date: Fri, 19 Oct 2018 09:17:59 +0530

Dear Prof. Case,
Are you implying that I need to separate my sugar portion and -OR group in
to two different unit files (in .mol2 format). If so wouldn't that affect
charge discrepancy?

On Thu, Oct 18, 2018 at 11:41 PM David Case <> wrote:

> 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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D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Thu Oct 18 2018 - 21:00:04 PDT
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