Hello again,
A belated thank you to Jason Swails for the imaging suggestions. However,
I still have mixed results trying to re-image into one correctly connected
molecule a two chain RNA structure (~100 nt total, chain1 ~30nt, chain2
~70nt) interacting via a kissing loop (KL). Following MD run with iwrap=1, the
pdb (produced by ambpdb from the restart file) intermittently
splits the structures from the trajectory file into two chains. The larger chain "sticks
out" of the solvent box around its half of the KL and is ROTATED relative to its initial
placement in the solvent box (by leap). The two stage re-centering and imaging
suggested below works for some states, when a smaller portion of the larger chain
is exposed outside the box (I tried the long and the short chain specs in the
first step, as well as only one-chain one step centering).
To avoid any misunderstandings on my side, is it possible not to
be able to re-image a split-chain molecule? If, for example, the RNA is rotated
relative to the box in such a way that one chain is still completely outside the box
following the iwrap=1 translation into the primary unit cell, is the below imaging scheme
going to fail ? Is that what "This will not always work" means? In short,
am I trying to do something impossible or am I still failing to do it the right way?
Also, I am still not clear on the role played by the topology file in the re-imaging.
I was able to re-image my RNA correctly from a trajectory run without iwrap=1,
but based on iwrap=1 restart (with a split primary cell image). That run was
writing only the RNA an ions to the trajectory file, and I used a topology file
without periodic box (and solvent flag) information in it with ptraj (re-imaging).
On a related issue; the whole iwrap=1 problem arose in response to restart
files not being able to accommodate large increases in absolute coordinates
in long MD simulations. I recall reading about plans to change the restart file
formatting limitations. Has it been done in the most recent release of Amber
(we are using Amber11) ?
Hope to lower my level of confusion. Thank you in advance,
Voytek Kasprzak
------------------------------------ from Jason Swails ----------------------------------
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).
---------------------------------------------------------------------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 20 2012 - 08:30:03 PDT
