Hi,
On Thu, Oct 31, 2013 at 9:45 AM, Jose Borreguero <borreguero.gmail.com> wrote:
> I am interested in Eab only. Thus, it would seem I have to get a parm +
> trajectory for only atoms from group A in order to get Ea (and similarly
> for group B), then do Eab=E-Ea-Eb?
This is correct. FYI, in cpptraj you can also use the 'outprefix'
keyword to print a stripped topology file that is compatible with your
stripped coordinates. For example:
parm AB.parm7
trajin AB.nc
strip :A outprefix B
trajout B.nc
will generate B.AB.parm7, which will be compatible with the output
trajectory B.nc. Make sure you are using an up to date version of
cpptraj.
-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)
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Received on Thu Oct 31 2013 - 09:00:05 PDT
