Dear Amber users,
I am doing unfolding for a 270-residue protein using Amber 9. By heating it
at 500K (dt=1.5fs), I observe its unfolded states (mostly by visualization
using VMD).
It's been running for 276 ns, but its active site is still somehow
"maintained" (not much changed --> I calculated distances among C-alpha
atoms of these active residues, the values are not very much different
among the unfolded states, e.g. the 6ns-state and the 240ns-state).
The overall RMSD significantly differ though.
This may be a "silly" question 'cause it is not a technical one, but I am
interested in it.
- I didnt put any restraint for the whole system during the unfolding, but
using iwrap=1 to keep it in the solvent box. Does this iwrap parameter
somewhat give any restraint per se?
- Im a newbie in unfolding such a big protein, how long normally does it
take to totally get unfolded protein? One of my professors folded a protein
in ms or second scale, how about unfolding?
- aside from heating, any other ways to unfold the protein? Is 500K an
appropriate value?
Thank you for any help. Any recommended papers are also very much
appreciated.
Regards,
Chinh
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Received on Thu Jun 07 2012 - 20:30:04 PDT
