AMBER Archive (2003)

Subject: frcmod file for Free energy perturbation tutorial of valine to alanine

From: dicksmit_at_umich.edu
Date: Fri Apr 04 2003 - 12:06:37 CST

Hi,

  I'm sorry I originally did not have a subject with this e-mail.
  I am using AMBER6 to work through the free energy perturbation tutorial that
mutates a valine to an alanine, however, AMBER6 does not have the frcmod file
for the dummy atom that is created. Could someone post the contents of this
file? I tried to create the file for the dummy atom, but I recieved an error
from xleap when I went to save the perturbed parameter file; it asked for
torsions that did not include the dummy atom to be included in the frcmod.
xleap suggested that these values be entered as zero, but wouldn't that change
the parameters for these torsions in the valine? Or, should these torsions be
entered in the frcmod as they appear in the force field?

Thank you,
Richard Smith