AMBER Archive (2004)

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

From: Bill Ross (
Date: Fri Feb 06 2004 - 16:21:12 CST

> > "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."

(For SiO2, that should probably be "Define a residue of 3 atoms.")

> > This is what I have done:
> >
> > 1. I inserted the "TER" card in the pdb after each
> > atom

If it's actually SiO2 and you did this for your entire array, you are
already misunderstanding the above. In any case:

Your 'base residue' should have only the minimum repeating unit of your
crystal structure. Once it is defined (including assigning atom types
and charges), save it as prep or lib file.

Then you add a TER after each 'base residue' in your pdb file and make
sure the residue name matches that of the 'base residue'. Then, when
the pdb is loaded, the template is applied to each residue.

> > 2. In leaprc.ff94 and in ff94.cmd I added "{ "Si"
> > "Si" "sp3" }" under addAtomType

(If both files are loaded, only leaprc.ff94 is needed.)

> > 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.
> What you need to do is the following: after you use loadPdb to read in
> your coordinates, use the "edit" command to edit your UNIT. This will
> bring up a graphical display. Use the left mouse button to select all atoms,
> then choose "edit selected atoms" from the pull-down menu. This will
> bring up a "spreadsheet" interface, where the atom types will be blank.
> You will need to enter the atom type into the blanks, and save things.
> Then you should be able to use the saveAmberParm command.

This is correct, my point above is to only do it for the 'base residue'
to avoid entering the atom definition for all the atoms in the xtal

Best to do a small saveamberparm test with the 'base residue' before
loading the pdb.


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