Hi,
If possible, could you send me the topology file and (non-imaged)
PDB/restart files of the frames you have trouble with so I can take a
look at them? This can be easily accomplished with cpptraj; say for
example frames 50, 67, and 110 are the problem frames:
parm system.top
trajin traj.nc
trajout problem.rst7 restart onlyframes 50,67,110
Thanks!
-Dan
On Fri, Jul 20, 2012 at 9:05 AM, Kasprzak, Wojciech (NIH/NCI) [C]
<kasprzaw.mail.nih.gov> wrote:
> 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
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 23 2012 - 08:30:02 PDT
