Im sorry, Dr. Simmerling, but I dont quite get what you meant "you should
also ensure that the results do not depend on the initial structure used"
in your previous reply.
Could you please make it a bit clearer?
Thank you.
Regards,
Chinh
On Thu, Jun 14, 2012 at 11:58 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> you need a box that can hold the unfolded state, not one that just
> fits the folded state.
> you should also ensure that the results do not depend on the initial
> structure used.
> hoestly, this is a very challenging problem, and difficult to do properly.
>
> On Mon, Jun 11, 2012 at 2:52 AM, Chinh Su Tran To
> <chinh.sutranto.gmail.com> wrote:
> > Dear Dr. Simmerling,
> >
> > I used the box size of 12 angstroms (doubted if it was large enough,
> > honestly). As visualized, the protein moved out to the box-edge though
> even
> > iwrap=1 was used.
> >
> > I wanted to detect the intermediate unfolded states, and the
> drug-targeting
> > ability at the active site of these intermediate unfolded states.
> > So what i need is the unfolded structures at different time points of the
> > unfolding pathway. And what I've got are unfolded representative
> structures
> > with significant "overall" RMSD differences. However, they dont satisfy
> > what I expected because the "little change" in the active site are
> actually
> > NOT able to represent the whole unfolding process, or in other words, I
> > havent got the "totally" unfolded conformations.
> >
> > Regarding to this scenario, could you please give me one advice that
> > whether I should jump in to change some parameter (i.e. increase the
> > temperature, or as you mentioned add the denaturants) to get the better
> > unfolded structures OR I need to start it over? I actually tried out
> > increasing temp to 600K at some time points (i.e. after the first 150ns),
> > but the total energy scenario changes.
> >
> > Thank you.
> >
> > Regards,
> > Chinh
> >
> > On Fri, Jun 8, 2012 at 5:57 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> it's not really an answer to your question, but have you considered
> >> the size box you need to hold the unfolded state? how large is your
> >> box? it may be that the protein is interacting strongly with its
> >> periodic images, stabilizing specific structures.
> >>
> >> regarding the "how long does it take"- proteins vary widely in this.
> >> is there experimental data for unfolding rate? that might give some
> >> clue, though of course it can't be done at 500K. there are other ways,
> >> such as adding denaturant, but keep in mind that unfolded states and
> >> pathways depend on the process sued to unfold it, and so what you do
> >> depends on what you want to learn. In my opinion, an unfolded protein
> >> at 500K doesn't really tell me much that has biological relevance.
> >>
> >> On Thu, Jun 7, 2012 at 11:17 PM, Chinh Su Tran To
> >> <chinh.sutranto.gmail.com> wrote:
> >> > 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 Sun Jun 17 2012 - 20:30:03 PDT
