Hi,
On Fri, Jul 29, 2016 at 6:26 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
>
> rms A first :1-88.C,CA,N rmsd.dat
> rms B first :288-328.C,CA,N rmsd.dat
> rms C first :1-88.C,CA,N rmsd.dat
You actually need to use the 'out' keyword before your output file
names (i.e. "out rmsd.dat").
>
> how should I define *first* for each and every trajectory?
You can use a 'reference' command to explicitly define the first frame
of each trajectory as a reference structure, e.g.:
parm A.prmtop
trajin A.mdcrd parm A.prmtop
reference A.mdcrd 1 parm A.prmtop [A_first]
...
rms A ref [A_first] :1-88.C,CA,B out rmsd.dat
...
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 Fri Jul 29 2016 - 08:00:02 PDT
