On Fri, Mar 8, 2013 at 7:51 AM, <dilrajl.bii.a-star.edu.sg> wrote:
> Dear Amber users,
> I have a query regarding centering of a tetrameric
> molecule during post processing of a simulated trajectory. I will be
> glad if you can kindly provide me with some insights on the problem
> that I am currently encountering in this regard.
>
> I have done simulation of a tetrameric complex in explicit water.
> After completing the simulation, I want to recenter the molecule into
> the primary box. The total number of residues in the complex is 396
> and each monomer comprises of the following residue set. (monomer-1:
> 1-184, monomer-2: 185-198, monomer-3: 199-382 and monomer-4: 383-396.
>
I would strongly suggest using cpptraj and the "autoimage" function (an
up-to-date AmberTools 12 is needed). Try this sequence of steps:
autoimage
center :1-396 mass origin
image origin center <familiar>
The latter two parts are necessary for centering the whole complex in the
periodic cell (autoimage centers only the first monomer and images
everything around that).
> SO for re-centering, I used the following command.
>
> trajin prod.mdcrd
> center :1-184 mass origin
> image origin center
> center :1-396 mass origin
> image origin center
>
For a tetramer you may have to do this in 4 steps if you don't want to use
the autoimage technique -- center the first monomer, then the first and
second, then the first through third, then the first through fourth
(imaging everything after that step). Also remember to use the "familiar"
keyword in the image command if you're not using an orthorhombic box.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 08 2013 - 05:30:03 PST
