Just a quick note on 'trajout' vs 'outtraj':
On Sun, Apr 27, 2014 at 7:50 AM, Jason Swails <jason.swails.gmail.com> wrote:
> trajin md2.mdcrd
> autoimage
> strip :WAT,Na+ outprefix stripped
> outtraj snapshot.pdb onlyframes 30000
> trajout md2_dry.mdcrd
This is correct and will work fine, but you don't really need
'outtraj' in this situation - two 'trajout' commands would be fine.
The 'outtraj' command is more for when you want to output structures
in the course of processing actions, whereas the 'trajout' command
always outputs structures after all actions have been processed. So
for example given this input:
trajin test1.nc
strip :WAT
outtraj Stripped.nc
trajout Fit-Stripped.nc
rms first out rms.all.dat
The 'outtraj' command here will write structures after they have been
stripped but before they have been rms-fit, while the 'trajout'
command will write structures that have been stripped *and* rms-fit.
-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) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 27 2014 - 13:30:02 PDT
