Dear Thomas Cheatham and Amber users,
Thanks for your suggestions.
I have used the following modification as per your suggestion.
I looks better, but the average rmsd is still in the 40s although the
fluctuations seems to appear in the acceptable range. Does it mean that the
protein has moved a lot during the initial phase of MD and then stabilized
around one structure? Is it meaningful?
If that is so, how can I calculate rmsd w.r.t. after a few frames (lets say
50th frame)?
Thanks.
ptraj file
--------
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 :2212 mass origin
image origin center familiar
rms first out 1fm9_fareqbr1.rmsd ':2112-2210'
--------
On Mon, Dec 5, 2011 at 11:02 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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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>
--
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 - 23:00:02 PST
