Hi,
On Mon, Apr 22, 2013 at 7:12 PM, nicolai petelski
<nico_petelski.hotmail.com> wrote:
> I am working with a cuaternary system (two saccharides, water and an aminoacid) using Amber 11 for simulation. I've made some cluster analysis with ptraj, but I have some problems with the understanding of the output results. Can any one suggest me how to read the output results?
It will be easier to help you if you ask more specific questions. In
general, I recommend reading through the description of the ptraj
cluster command in the AmberTools manual (in the AT12 manual I have it
starts on page 513), as well as reading through the following
reference:
Shao, J.; Tanner, S.W.; Thompson, N.; Cheatham, T.E. III. Clustering
molecular dynamics trajectories: 1. Characterizing the performance of
different clustering algorithms. J. Chem. Theory Comput., 2007, 3,
2312–2334.
-Dan
> Waiting for your valuable reply.
> Thanks in advance
> Best regards Nicolai Petelski
>
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--
-------------------------
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 Tue Apr 23 2013 - 07:30:04 PDT
