AMBER Archive (2000)

Subject: Protein and Ligand in Leap

From: David Bevan (drbevan_at_vt.edu)
Date: Thu Apr 06 2000 - 10:56:51 CDT

I have a complex of a protein with a ligand that I have read into Leap so
that I can solvate, prepare coordinate and topology files, etc. When I view
the complex in the Leap Unit Editor window, the protein and ligand are far
apart in the display, rather than being complexed. This occurred when
reading in the whole complex as one PDB file and also when reading in
separate PDB files and using the "combine" command. The protein and ligand
appear as a complex in another viewing program, and based on the
coordinates, the molecules should be complexed. Any idea on why Leap
separates the protein and ligand?

David Bevan

David R. Bevan
Dept. of Biochemistry
201 Fralin Biotechnology Center
Virginia Tech
Blacksburg, VA 24061

Phone: (540) 231-5040
FAX: (540) 231-9070