On Tue, Jul 17, 2012 at 10:30 AM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
>
> Hello,
>
> I am running Amber 11 (sander) simulations of an RNA complex with two
> chains
> connected by a kissing loop (in explicit solvent). The solute drifts fast
> enough to yield
> restart files with the "death stars" due to coordinates being out of range
> well
> before the trajectory is of the desired length.
>
> I employed iwrap=1 flag to get the coordinates "wrapped" into the primary
> box.
>
> However, what is happening - as monitored by "ambpdb" and ptraj - is that
> for periods of time the two chains get separated and packed into the the
> primary
> box side-by-side (sardine style). The physics of the simulation is not
> affected to the
> best of my understanding, but extracting the corrected image - and
> calculating RMS
> for that matter - has eluded me so far. I tried ptraj with "center
> :1-100" (total RNA
> for both chains) or center based on various selected nucleotides, and
> "image familiar",
> but the only thing I can affect is the relative placement of the separated
> chains (which
> remain separated)
>
This will not always work, because you're centering on 2 strands of RNA.
If they are separated on either side of the box, then the COM (or COG)
will be in the center of the box, and ptraj will continue to think that the
current image is the one you want (note there is no 'correct' imaging,
given the infinite periodicity of the system and the arbitrariness of the
'absolute' location of the periodic cell boundaries).
What you should do is center on ONE RNA strand and image everything around
that. This will pull the other RNA strand into place alongside it. If you
then want the whole duplex to be centered (rather than just that one
strand), you will have to image one more time, this time centering both
strands. So your ptraj script will look something like this (assuming each
RNA strand is 50 residues):
center :1-50 origin mass
image origin center [familiar]
# To center the whole thing
center :1-100 origin mass
image origin center [familiar]
This should fix your imaging issues. Note that 'familiar' is necessary for
triclinic cells (if you have an orthorhombic cell, do not put familiar).
HTH,
Jason
P.S., If you were at all unsure, the 'wrapping' has no effect on the
physics of the simulation, since Amber uses the "minimum image convention"
and the system is replicated infinitely in all directions.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jul 17 2012 - 08:30:03 PDT
