RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated

From: Steve Spronk <>
Date: Thu, 29 Nov 2007 09:44:33 -0500

Another addition to the discussion, also referring back to your solvatebox
vs. solvateoct question:

One thing to be aware of when using a rectangular box instead of a truncated
octahedron (which is much more spherical in shape) is that the rectangular
box probably has different lengths in different dimensions. If you are
simulating a soluble protein, there is nothing to prevent it from rotating
during the simulation. The box, however, does not rotate; the protein may
rotate so that its "longest" dimension no longer coincides with the box's
longest dimension. The distance between the protein and the box edge--which
was originally 12 A using the parameters you described--may now be much
less, and in fact, the protein may actually span the whole box. You end up
inadvertently violating the minimum-image convention. This is especially
problematic for "elongated" structures, such as a stretch of DNA or a linear
polymer. It's a tough issue, because these systems are most prone to the
minimum image violations I've just described, but they also result in the
most "wasted" space when placing them in an octahedral box.

The membrane in your system will not allow for this type of 3-dimensional
rotation in your simulation, so you are safe using the rectangular box,
which gives you the fewest number of particles to deal with. But it is
often preferable to use a truncated octahedron for long simulations of
soluble proteins, even if it requires more water molecules.

-----Original Message-----
From: [] On Behalf Of
Francesco Pietra
Sent: Wednesday, November 28, 2007 10:02 AM
To: Amber
Subject: AMBER: Equilibration of protein complex in POPC membrane, the whole
TIP3 solvated

Referring to subject, I had no answer to my question if solvate box (added
21847 residues, density 0.792) is preferable to solvateoct (added 30286
residues, density 0.867). Therefore, I assume this means carrying out MD

My question now is how to carry out equilibration for this system. The pore
protein entails a docked large ligand (118 atoms) within the pore, coming
amber rescore in DOCK. It was immersed in a POPC membrane, where the polar
heads of POPC are solvated TIP3P. Then the whole was TIP3PBOX solvated with
12.0 A buffer.

Summing up all that I could learn from the literature,I guess that the
should be first energy minimized with protein-complex restrain (SHAKE on H
atoms and PME). For membrane I found indications of ca. 30 kcal/molxA^2. No
idea how that could be applied to my protein-complex.

Once that (or a more reasonable) pre-equilibration is carried out, I suppose
have to gradually "heat" the system to 300K at constant volume. Here surely
protein complex should be restrained as above. However, probably the POPC
molecules should also be restrained (or only their polar head?).

With this second step (or a more reasonable one) the system should be ready
pre-MD at 300K and 1 atm, initially with the above restrain on the protein
complex (and probably the lipid). Gradually (after how many ps?) restraint
the protein (and lipid, if any was applied) should be removed.

Now the system should be ready for production MD, under SHAKE for H atoms.

In view of the computational burden, I would appreciate any guidance.

francesco pietra

Be a better pen pal.
Text or chat with friends inside Yahoo! Mail. See how.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 02 2007 - 06:07:19 PST
Custom Search