[AMBER] RMSD ptaj difficulty

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Mon, 5 Dec 2011 10:48:25 +0530

Dear Amber users,
I want to calculate backbone rmsd for selected residues using ptraj, as vmd
is not able to load all trajectories due to less memory.

I have prepared files as shown below:
But I'm getting very high rmsd (upto 40-60 angstrom) values. It is not
making any difference whether I do center image or not.
I want to know if the results are reliable? If not where I might possibly
be making a mistake.

How can I get rmsd with respect to time in picoseconds using amber tools?

ptraj command:
ptraj 1fm9_far.prmtop < measure_fareqbr_rmsd.in

ptraj file measure_fareqbr_rmsd.in 
----
trajin
/home/vaibhav/vaibhav_data/amber/1fm9_far/1fm9_MD_runs/1fm9_far_3nMD_1.mdcrd
1 1500 1
reference
/home/vaibhav/vaibhav_data/amber/1fm9_far/1fm9_MD_runs/1fm9_far_equil.restrt
center
':2112,2113,2114,2122,2123,2124,2129,2130,2131,2137,2138,2139,2145,2146,2147,2154,2155,2156,2163,2164,2165,2171,2172,2173,2183,2184,2185,2191,2192,2193,2200,2201,2202,2208,2209,2210'
image
':2112,2113,2114,2122,2123,2124,2129,2130,2131,2137,2138,2139,2145,2146,2147,2154,2155,2156,2163,2164,2165,2171,2172,2173,2183,2184,2185,2191,2192,2193,2200,2201,2202,2208,2209,2210'
rms reference out 1fm9_fareqbr.rmsd
':2112,2113,2114,2122,2123,2124,2129,2130,2131,2137,2138,2139,2145,2146,2147,2154,2155,2156,2163,2164,2165,2171,2172,2173,2183,2184,2185,2191,2192,2193,2200,2201,2202,2208,2209,2210'
-----
-- 
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Sun Dec 04 2011 - 21:30:03 PST
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