Re: [AMBER] simulations in urea

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 3 Jul 2010 10:58:38 -0700

> i am simulating a protein dimer in 8M urea and i just want to
> have some suggestions
> about the results if anybody has ever experienced.
> few things i want to share are:
> first: is the urea box a kind of slab distributed in parts
> means not a complete
> box and oly after continuing simulations further it gets uniformed?

It would help to see mdin files for the equilibration, e.g. did
you do constant pressure to reach density of 1? Do you have iwrap=1?
If you send a picture of the structure we can see what you mean.

> second: i expect my protein to unfold in 8M urea as i have
> seen in my solution studies.

What is the time scale for this experimentally?
Is it a practical time to simulate?

> so can i expect my dimer protein to be separated in monomers. i mean
> shall i remove periodic boundary or not?

If you expect your dimer to split in two, again what is the
expected time scale, and is there enough urea/water to solvate
the whole system with distance between the parts?

> by far upto 2ns i only observed some of the secondary structure distortions
> thats it.

My impression is that processes you are studying may take place on
much longer time scales.


> any help or any link to these kind of studies will be really commendable.
> thanx in advance
> hope to get reply from all

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Received on Sat Jul 03 2010 - 11:00:05 PDT
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