AMBER Archive (2004)

Subject: AMBER: Lattice structures in xleap

From: Brandon Tefft (bjtefft_at_yahoo.com)
Date: Mon Jan 26 2004 - 23:11:46 CST

Hello. I am an undergraduate and I have been working with AMBER for a few months now. I have a silicon dioxide lattice structure (with thousands of atoms) described in a .pdb file and I am trying to get xleap to output the appropriate .inpcrd and .prmtop files for use with sander. I don't need any bonding definitions for the lattice because I am going to fix those atoms in space anyway, so I believe xleap will work for my purposes. 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? I would greatly appreciate any help. Thank you in advance.
 
Brandon J. Tefft
Junior, General Engineering
University of Illinois at Urbana-Champaign

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