Thanks. I eventually caught the missing space.
On Wed, Nov 20, 2013 at 10:54 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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:
> > ante-MMPBSA.py -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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
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 - 09:30:02 PST
