Re: [AMBER] regarding forcefield for rna

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 12 Jun 2010 12:57:04 -0700

> I am giving you the attachment which shows how it comes apart dynamically.

I see MD1, then a bunch of MDe's that look the same, then MD2
showing great separation. If these are all the same number of
ps apart, then it looks like the separation may have occurred
due to imaging of one strand whereby it gets shifted across
the box but still remains in complex across the box boundary.
You can test for this conclusively by saving every step to
mdcrd and determining if the jump happens in one frame.

If it's imaging, ptraj can reassemble them with the 'image'
command (I have never done this myself). However it is odd that
it could drift to the edge of the box. What water clearance did
you use? Again, it would be interesting to see how you equilibrated
(mdin files).

A deeper issue is that it looks like MD1 is not in quadruplex
formation - did it previously start out as such? What is the
actual sequence?


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Received on Sat Jun 12 2010 - 13:00:08 PDT
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