AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Nov 29 2007 - 09:44:33 CST

--- Steve Spronk <spronk_at_umich.edu> wrote:

> 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.

It has indeed:

Total bounding box for atom centers 110 107 89

as the POPC membrane has also different lengths (only xy can be given on
building that).

> 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.

That is very much to take into account.

>
> 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,

This is what I suspected (better, hoped). Good that the behavior is that
indeed.

> 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.

As I was just wondering about the initial minimization (taking into account
yesterday suggestions by Bud Dobson and Gustavo Seabra, as well as Ross Walker
tutorial 1B), I take the opportunity to ask about that, in particular the
cutoff

imin =1,
maxcycl = 2000,
ncycl = 1000,
ntb = 1,
ntr = 1,
cut = ?
/
Hold protein-ligand fixed
30.0
RES 1 446
END
END

CUT: cut should be less than the smallestbox dimension (89) but, I suppose,
more that half the longest dimension of the protein. How to keep on the safe
side? On certain literature (not Amber) I have seen carrying out MD by
restraining everything out of a sphere centered on the protein, the sphere not
encompassing the whole protein, immersed in a lipid and TIP3P solvated. It must
have been to reduce the burden of the calculation. However, I rely in having
removed all lipid and water from the region occupied by the protein.

Thanks for any suggestion about the protocol for the initial minimization.

francesco

>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] 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
> with
> solvatebox.
>
> 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
> from
> 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
> system
> 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
> to
> have to gradually "heat" the system to 300K at constant volume. Here surely
> the
> 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
> for
> 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
> on
> 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.
>
> Thanks
> francesco pietra
>
>
>
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