The 'crdset' keyword in this command:
> average crdset cpu-average.pdb pdb
specifies that you want to save the average as a COORDS data set, not
write it to a file. Are you sure this actually runs? If I give similar
input I get this error:
Error: [average] Not all arguments handled: [ pdb ]
Make sure you're using the most up to date version of cpptraj (16).
Since you're saving the average structure (which you want to use as a
reference) as a COORDS data set, you should specify that in the RMS
command. Also note that 'reference' is a ptraj-backwards-compatible
keyword that means "use file loaded as reference", so it doesn't apply
here; you want 'ref'. So changing your 'average' command to something
like:
average crdset cpu-average
and your 'rms' command to:
crdaction md2_cpu_average rms ref cpu-average :1-340&!.H=
Should work.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 09 2016 - 12:00:04 PDT
