AMBER Archive (2006)

Subject: Re: AMBER: question on protein folding simulation

From: Noriaki Okimoto (
Date: Sun Dec 03 2006 - 20:43:11 CST

Thanks for that ideas.
I am afraid that these ideas don't consider the velocities of protein
and hydrated water atoms.
In reducing system size, is there no need to worry about it?

Noriaki Okimoto

>Dear Noriaki Okimoto:
>You need to write a program to remove those water molecules that are away
>from the solute after you image the system first so that all water molecules
>are within the new and smaller box. You then need to change the topology
>file. There are two ways to do this.
>1) Write a program to read-in the topology file and remove those paramters
>associated with the excess water molecules. The atoms are numbered in such
>way that solute appears first. I personally prefer this approach because it
>provides an excellent opportunity to learn AMBER which may be helpful in
>2) You can generate a PDB file from the modified restart file. Then, you can
>read-in the PDB by leap to regenerate the topology file (don't forget to
>"setbox"). This is definitely a (much) simpler approach.
>After you build the system, you need to hold the protein for a short while
>to allow the water to re-equilibrate (10-100ps in more than sufficient).
>Keep in mind that the protein is likely to expand later. So, you probably
>should not be too aggressive in cutting the size. In case that the protein
>expands too much, you need to add some water molecules back. You can use
>those water molecules that you removed. But you then have to "expand" a
>little bit because the removed "skin" and the smaller system are not
>entirely compatible (because waters move around).
>Good luck!
>>-----Original Message-----
>>[] On Behalf Of Noriaki Okimoto
>>Sent: Friday, December 01, 2006 4:01 AM
>>Subject: AMBER: question on protein folding simulation
>>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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