From: Milo Westler <milo.nmrfam.wisc.edu>
Date: Wed, 20 Nov 2013 10:34:23 -0600

  I've been trying to use ante-MMPBSA to create complex, receptor, and
ligand from a solvated protein-DNA complex topology file that I have used
in MD simulations.

My input is:
ante-MMPBSA.py -p prmtop -c complex -r receptor -l ligand -s ':Na+,:WAT'-n

The ligand mask, -n ':1-84', represents the protein. Residues 85-108 are
the DNA and prmtop is a topology file that I have successfully used for the

With this input I get:
Error: Unknown command-line arguments: :1-84

If I only strip the Na+ and WAT, the program runs successfully.

What am I doing wrong?

-- Milo
National Magnetic Resonance Facility at Madison
      An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
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Received on Wed Nov 20 2013 - 09:00:03 PST
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