Hi,
On Thu, Dec 13, 2012 at 3:09 AM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> It turns out that when I use a prmtop file as 'parm', instead of a pdb
> file, then it works fine for me too.
This makes sense to me since the 'byres' average over residues is
currently mass-weighted by default, and there are no masses in the PDB
file (I had actually fixed this issue a while back in the current
development version of cpptraj).
> I'm happy to just create 'stripped' prmtops and use those for my analysis.
Just FYI you can easily do this with cpptraj when you use the 'strip'
command, e.g.
parm protein.parm7
strip :WAT outprefix nowat
trajout nowat.nc netcdf
will get you your stripped trajectory (nowat.nc) and a matching
stripped parm (nowat.protein.parm7).
Thanks for the report.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Dec 13 2012 - 08:30:02 PST
