Dear Dr. Steinbrecher,
Your explanation is very clear and helpful. Thank you very much.
I think I should start to pull my protein apart manually, heat it, then run
MD again.
"Please consider that what you are trying to do is not a standard
simulation by any means, by prepared to invest lots of brain and computer
power to get something worthwhile here..."
Thank you for your advice. Hope I will learn something from this too.
Thank you Dr. Steinbrecher.
Regards,
Chinsu
On Mon, Sep 19, 2011 at 7:22 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > 1. In VMD, I loaded the prmtop file then followed by the AMBER restart
> > (for
> > *rst)* or AMBER coordinate (for *crd)* accordingly. For this point, I am
> > checking again the options to open in VMD, something related to implicit
> > solvent and periodic simulation.
>
> Load type crd vs. crdbox is a likely culprit...
>
> > 2. I wanted to unfold my protein using heating (from 0K to 400K)
> gradually
> > in 50ps, then MD has been running for re-folding it (temp from 400K down
> > to
> > 300K and keep 300K for equilibration) in ~ 60ns (it is still running
> now).
> > I want to detect the folding simulation, but because my protein is quite
> > big
> > (158 aa), and I think it is infeasible to fold it from scratch (from its
> > sequence), so I started with a process of unfolding a homology model, and
> > make it re-fold again.
>
> This goes beyond technical help and into my personal scientific opinion,
> but I do believe it unlikely that an unfolded protein will spontaneously
> fold in 60 ns. If you unfold it completely first, it will not retain any
> 'memory' of the folded state and therefore not fold any quicker than a
> random starting structure. Or, phrased differently, if after your
> unfolding the protein *does* retain a preference to fold right back, your
> unfolding was not complete.
>
> > I hope my reasoning is not so wrong so far. As you said, it was NOT
> > unfolded, so will you suggest me to increase the temperature to heat it
> up
> > OR could you give me some suggestion to unfold it please?
>
> if you go even higher in T, you may run into simulation stability problems
> at some point. Your initial unfolding run is only 50ps! Simulating (much,
> much) longer could help the unfolding process. Alternatively, adding
> forces to pull e.g. the termini apart will force unfolding as well...
>
> Please consider that what you are trying to do is not a standard
> simulation by any means, by prepared to invest lots of brain and computer
> power to get something worthwhile here...
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Mon Sep 19 2011 - 20:00:04 PDT
