As part of developing parameters to describe ligand molecules that we want to include in MD calculations in AMBER, we are attempting to compare the frequencies and associated normal modes from gaussian with those from the nmode module of AMBER. We want to be certain that the normal mode for any given frequency from gaussian corresponds to the same normal mode for a comparable frequency in nmode. From the gaussian output, we are able to visualize the normal modes using the program molekel. Does anyone know if there is any comparable way to visualize the output from nmode/nmanal? Thanks.
David Bevan
David R. Bevan, Ph.D.
Dept. of Biochemistry
201 Fralin Biotechnology Center
Virginia Tech
Blacksburg, VA 24061
Phone: (540) 231-5040
FAX: (540) 231-9070
Received on Mon Jun 11 2001 - 10:36:39 PDT
