RE: AMBER: question on protein folding simulation

From: Yong Duan <>
Date: Fri, 1 Dec 2006 10:32:58 -0800

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-----
> 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 Sun Dec 03 2006 - 06:07:56 PST
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