Re: AMBER: question on protein folding simulation

From: Carlos Simmerling <>
Date: Mon, 04 Dec 2006 07:32:16 -0500

the restart file has velocities, so if you use that then you will
consider velocities.

Noriaki Okimoto wrote:

> Hi.
> 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?
> Regards,
> 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
>> future.
>> 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!
>> yong
>>> -----Original Message-----
>>> From: [] On
>>> Behalf Of Noriaki Okimoto
>>> Sent: Friday, December 01, 2006 4:01 AM
>>> To:
>>> 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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Received on Wed Dec 06 2006 - 06:07:28 PST
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