AMBER Archive (2004)

Subject: Re: AMBER: Could not assign parameters

From: Sivanesan Dakshanamurthy (sd233_at_georgetown.edu)
Date: Fri Jun 18 2004 - 14:35:32 CDT

Dear Dr. David A. Case:
Thank you very much.
Siva

D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center (NCI Comprehensive Cancer Center),
Georgetown University, DC 20057
Phone: 202-687-6338

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Friday, June 18, 2004 3:04 pm
Subject: Re: AMBER: Could not assign parameters

> On Fri, Jun 18, 2004, Sivanesan Dakshanamurthy wrote:
> >
> > I am trying to run tleap for the given protein that contains
> ligand. But
> > when I ran tleap, the following error occur for all protein
> atoms including
> > ligand atoms:
> > ____________________________________________________
> > ................
> > ............
> > FATAL: Atom .R<OHT 553>.A<H102 31> does not have a type.
>
> By default, Amber knows about proteins and nucleic acids, but not
> aboutmost ligands. You will need to create a library that
> describes your ligand.
> This is most conveniently done using the antechamber program.
> Some ligands
> may be found in the "contributed parameters" link at the Amber
> home page.
>
> ...good luck...dac
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