On Fri, Sep 07, 2012, Buback, Clayton (S&T-Student) wrote:
>
> I am trying to use Amber to run simulations on a large
> non-biomacromolecule containing around 14,000 atoms. The molecule is
> novel, and I have created my own PDB file to run. All atoms are recorded
> as HETATM, and all located in one residue (also novel) called X5Q.
You have to create a library file for each novel entity, telling LEaP how to
construct a force field representation. See Tutorial B4 to get started.
Basically, LEaP has no intelligence: it is simply a bookkeeping program that
matches atoms and residues in your PDB file with atoms and residues in a
template library. (Type "list" at the tleap prompt to see what it knows about
by default.) If you have novel things, you have to create libraries that
describe them.
....dac
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Received on Fri Sep 07 2012 - 07:30:02 PDT
