Hi,
On Wed, Aug 21, 2013 at 10:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Note that
> you *must* ensure the same number of atoms is selected in the target
> mask and the reference mask (otherwise the RMSD makes no sense).
FYI, you can test mask selections in cpptraj using the 'select' or
'parminfo' commands. The former gives less info, the latter much more
info. This is easiest to do in interactive mode. For example:
> parm tz2.parm7
AmberParm Title: []
Warning: [tz2.parm7] ATOMIC_NUMBER not present in topology.
> select :1
Selected 13 atoms.
Selected= 1 2 3 4 5 6 7 8 9 10 11 12 13
> parminfo :1&!.H=
#Atom Name #Res Name #Mol Type Charge Mass
1 N 1 SER 1 N3 0.1849 14.0100
5 CA 1 SER 1 CT 0.0567 12.0100
7 CB 1 SER 1 CT 0.2596 12.0100
10 OG 1 SER 1 OH -0.6714 16.0000
12 C 1 SER 1 C 0.6163 12.0100
13 O 1 SER 1 O -0.5722 16.0000
Hope this helps,
-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 Wed Aug 21 2013 - 22:30:03 PDT
