Re: AMBER: Lattice structures in xleap

From: Bill Ross <>
Date: Mon, 26 Jan 2004 23:52:38 -0800 (PST)

> I have a silicon dioxide lattice structure (with thousands of atoms)
> described in a .pdb file ...
> My problem is that xleap requires a "type" for each atom
> and the standard libraries don't seem to provide them.
> How is it that I can associate my .pdb file's atom names
> with the appropriate type, element, and hybridization without
> typing them all in by hand?
E.g. for an array of silicon atoms:

Define a residue of one atom. Make up a type name for that atom.
Save the residue definition to a file and reload it whenever
running leap for this situation. Define mass and vdw params for
the new atom type in a frcmod file, and load it whenever needed.

Make sure there is a TER card in the pdb after each atom. When
the pdb is loaded, the atom type will be applied to each atom.

You will also need to assign the element and hbridization to the
new atom type, see the standard leaprc files for an example.

Bill Ross

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Received on Tue Jan 27 2004 - 08:53:01 PST
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