AMBER Archive (2006)

Subject: Re: AMBER: question on protein folding simulation

From: Noriaki Okimoto (okimoto_at_gsc.riken.jp)
Date: Sun Dec 03 2006 - 20:51:17 CST

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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