AMBER Archive (2004)

Subject: Fwd: Re: AMBER: Lattice structures in xleap

From: Brandon Tefft (bjtefft_at_yahoo.com)
Date: Fri Feb 06 2004 - 15:27:50 CST

Amber users-
     Thank you for the reply, however, I am still
having trouble coordinating my silicon lattice pdb
file with xleap. I think the step I'm missing is the
advice to:

"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."

This is what I have done:

1. I inserted the "TER" card in the pdb after each
atom
2. In leaprc.ff94 and in ff94.cmd I added "{ "Si"
"Si" "sp3" }" under addAtomType
3. In parm94.dat I added the two Si Lennard-Jones
constants

     I'm not sure weather or not those changes defined
the atom type I need. As it is now, xleap is reading
in the silicon atoms, but not assigning a type to
them. I, therefore, cannot get the inpcrd and prmtop
files I need for sander. Again, I don't need any
bonding interactions between the silicon atoms because
I am just going to hold them fixed in space during the
dynamics. Thank you for your help!

Brandon J. Tefft
Junior, General Engineering
University of Illinois at Urbana-Champaign

--- Bill Ross <ross_at_cgl.ucsf.edu> wrote:
> Date: Mon, 26 Jan 2004 23:52:38 -0800 (PST)
> From: Bill Ross <ross_at_cgl.ucsf.edu>
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Lattice structures in xleap
>
> > 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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