AMBER Archive (2007)

Subject: Re: AMBER: carbohydrate-peptide

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 21 2007 - 18:04:59 CST

On Mon, Feb 19, 2007, Beale, John wrote:

> Can someone point me in the right direction? How does one build a
> molecule by connecting any arbitrary sugar unit to a peptide structure?
> I can easily build the pdb file for the structure that I want in SYBYL,
> but it never loads in LEaP. How are the forcefields handled in AMBER
> (e.g. FF03 for the peptide and GLYCAMXX for the sugar)? Do you load both
> of them at the same time?
>

It is easy (and expected) to load both glycam and a protein force field at the
same time. You do have to take some care that the atom and residue names in
your pdb file match those in the Amber libraries. Without knowing why "it
never loads in LEaP" it is hard to be more specific.

...good luck...dac
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