On Fri, Feb 06, 2004, Brandon Tefft wrote:
> 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.
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.
Also, to avoid having to do the editing step again, it might be a good
idea to use saveOff to save you unit into an off file. You can load this
again later, and the atom types will be defined.
....hope this helps...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri Feb 06 2004 - 22:53:01 PST
