AMBER Archive (2006)

Subject: Re: AMBER: question on protein folding simulation

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Mon Dec 04 2006 - 18:47:32 CST

Another method, can you get a pdb file of a simulation
with explicit water molecules, at some stage, you
totally remove the water and get a new pdb file, then
run another md with explicit water molecules?

Best regards.

Fenghui Fan

--- Noriaki Okimoto <okimoto_at_gsc.riken.jp> wrote:

> Hi.
> Thanks for your reply.
> Now I would like to try folding simulation with
> using explicit water
> molecules.
>
> Anyway, thanks.
>
> Regards,
> Noriaki Okimoto
>
> >I donot know whether I am right. Can you di the
> >simulation without water box, and after it is
> >partially folded, you add a water box? Maybe this
> >method will be much better.
> >
> >Best regards.
> >
> >Fenghui Fan
> >
> >
> >--- Noriaki Okimoto <okimoto_at_gsc.riken.jp> wrote:
> >
> >
> >
> >>Hi amber users,
> >>
> >> I am going to try protein folding simulations. My
> >>target protein consists of 35 amino acid residues.
> >>At first, I am going to perform folding
> simulations
> >>from extended structure with a periodic boundary
> >>system. After it will collapse and pack compactly
> in
> >>the simulation, I would like to reduce the system
> >>size (that is, reduce number of water molecules in
> >>the system) and continue to perform the folding
> >>simulation from the reduced system, because the
> >>system size with the extended structure is very
> >>large. In reducing system size, I would like to
> >>treat hydrated water molecules around the peptide
> >>with those velocities obtained from simulations of
> >>the extended peptide. But I have no proper and
> >>cleaver idea on reducing the system size.
> >> One idea is that new water molecules are
> generated
> >>by using leap module, and then those only new
> water
> >>molecules are equilibrated by short simulation
> >>(several tens of pico seconds) with restraining
> >>motion of peptide, to obtain start system for
> >>continuous folding simulation. Is this way proper?
> >>
> >> Does anybody could help me and give the advice to
> >>reduce the periodic system size for protein
> folding
> >>simulation.
> >>
> >> Thank you in advance.
> >>
> >> Noriaki Okimoto
> >>
> >>
> >>
> >>
>
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> >
> >
> >
> >
>
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