Re: [AMBER] Parametarization error

From: senal dinuka <senal.ichemc.edu.lk>
Date: Thu, 18 Oct 2018 12:48:16 +0530

As per your suggestion I prepared the prep file and separately carried out
tleap for the ligand portion only. connectivity and naming for sugar
portion named 0GB is shown to be available but for the portion of ligand
named UNK, it is still missing. Here I have attached the extracted ligand,
prep file and its tleap script. Is it possible to work with two residue
names like here. If so am I doing it the correct way? I appreciate your
suggestion

Regards,

On Thu, Oct 18, 2018 at 10:16 AM Bill Ross <ross.cgl.ucsf.edu> wrote:

> > 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.
>
> Bill
>
> 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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-- 
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678







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Received on Thu Oct 18 2018 - 00:30:03 PDT
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