> 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.
...
>
> ptraj command:
> ptraj 1fm9_far.prmtop < 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
Skip the reference for now, try rms first... I think reference only reads
PDB.
> 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'
Why such a large disparate set of residues? Perhaps center :2112-2210 ?
> 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'
You want to image *all* residues, not just those you chose... The center
chooses where atoms are imaged around, then you want to move all residues
not just those in that selection... Try,
center :2212 mass origin
image origin center familiar
rms first out 1fm9_fareqbr.rmsd
--tec3
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Received on Sun Dec 04 2011 - 22:00:03 PST
