Hi,
On Wed, Feb 6, 2013 at 10:58 AM, Cassandra Churchill
<churchil.ualberta.ca> wrote:
> Following the simulation of a system for 15ns (trajectory file of 75 000 frames), I am attempting to analyze the trajectory with an RMSD calculation with ptraj. After reading in the trajectory files and striping the solvent and ions, I use the commands "center .CA mass origin" and "image origin center, and then calculate the mass weighted RMSD with respect to the first frame in 3 ways: (1) of C-alpha atoms, (2) of the protein backbone, (3) of all atoms.
You have to be very careful when combining 'strip', 'image' and
'rmsd'. Without seeing your exact input to ptraj I can't make specific
recommendations, but in general this is the procedure I follow: First
strip, image, and output the stripped trajectory for analysis. The
reason to perform imaging before or during a strip phase is because
imaging requires box information, which you typically get rid of when
stripping. Also, I recommend you use cpptraj and 'autoimage' for
imaging, since imaging in ptraj can require extensive care to avoid
imaging artifacts. For example:
Step1 (cpptraj):
parm prmtop
trajin mdcrd.nc
strip :WAT,Na+,Cl- outprefix nowat
autoimage
trajout nowat.mdcrd.nc netcdf nobox
This will generate an imaged/stripped trajectory with no box info
named 'nowat.mdcrd.nc' and a corresponding topology named
'nowat.prmtop'. This has the added benefit that subsequent analysis
using 'nowat.mdcrd.nc' will be much faster. After I have a stripped
and imaged trajectory, then I perform any analysis (like RMSD):
Step2 (cpptraj):
parm nowat.prmtop
trajin nowat.mdcrd.nc
rms Calpha .CA first out rms-CA.dat
> To further attempt to isolate this problem, I obtained the pdb for frame 60521 from the trajectory, and some of the coordinates in this pdb are 0.000.
If this is from the original trajectory, the frames in question are
likely corrupted. If you're using netcdf trajectories you can safely
discard corrupted frames and perform analysis on the non-corrupted
frames. However, if you're using ascii trajectories it's much harder
to recover frames after corruption occurs.
-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 Feb 06 2013 - 11:00:02 PST
