Hi,
On Thu, Dec 6, 2012 at 5:05 AM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Is this a correct procedure to follow or should I fit the trajectory to the
> average structure?
You should definitely fit to an average structure if you are going to
be calculating b-factors.
> Do I still have to include the "image center" keywords?
Only if you observe imaging artifacts in your trajectory (this will
not be fixed by RMS fitting). These usually show up as very large
jumps in the global RMSD.
> Is it meaningful to cluster the frames with an interval of 10ps or more
> (using sieve keyword)?
The answer here varies. In general this should be OK, but you should
always pay careful attention to your results to make sure they make
sense. My feeling is that a sieve of 10 on 25000 frames should be OK.
If you're worried about potential periodicity artifacts you can 'sieve
random'.
> Is it necessary to do an RMS fit of the whole trajectory before performing
> clustering analysis?
No - frames are RMS fit to each other.
-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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 12 2012 - 11:00:03 PST
