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)
Is it a bug or a feature? Is there a combination of ptraj arguments that would
control it? The only "method" I found so far is to run simulations without the
iwrap=1 flag and periodically try short restarts with iwrap=1 in hope of "catching"
the right state which wraps the two chains back to the primary box without separating
them, thus buying more time before the restart files get corrupted. Needless to say,
it is a game of chance, not a protocol.
Any help or info that nothing can be done about this would be appreciated.
Thank you, Voytek Kasprzak
Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, SAIC-Frederick, Inc.
Frederick National Laboratory for Cancer Research, Frederick, MD.
(301) 846 5537
www.ccrnp.ncifcrf.gov/~kasprzak
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Received on Tue Jul 17 2012 - 08:00:03 PDT
