Hi Dan,
Thanks a lot. It now works just the way I wanted.
Regards,
Moitrayee
> 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 Thu Aug 22 2013 - 00:00:02 PDT
