From: Jason Swails <>
Date: Wed, 20 Nov 2013 11:54:03 -0500

On Wed, 2013-11-20 at 10:34 -0600, Milo Westler wrote:
> Hi,
> 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:
> -p prmtop -c complex -r receptor -l ligand -s ':Na+,:WAT'-n
> ':1-84'

You're missing a space: ':Na+,:WAT'-n

The "-n" is interpreted as part of the ligand mask, and as a result does
not recognize ':1-84' as a valid command-line argument.

Also, this will assign your protein to the prmtop file "ligand" and will
assign your DNA to the prmtop file "receptor."

Specifying "-m ':1-84'" instead will reverse this. Of course the label
doesn't mean anything really (as long as your interpretation of the
results is appropriately adjusted), but since it's unusual in my
experience to have this designation I just thought I'd point it out.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 20 2013 - 09:00:04 PST
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