Just a reality check question. Is the interface actually coming apart
or do you have an imaging problem. I.e. are you seeing a gradual
separation or does your protein just wrap to the next cell and
suddenly one or two monomers is on the other side of the box?
In my dimer simulations I have to be careful about imaging, especially
with iwrap turned on. To prevent the protein from splitting apart at
the cell boundaries.
Melinda Layten
On 1/22/08, Irene Newhouse <einew.hotmail.com> wrote:
> I've had a multimeric protein fall apart in NAMD. When I brought the solvent
> ionic strength up to 0.15M with NaCl, the subunits stayed together.
>
> Irene Newhouse
>
> > Date: Tue, 22 Jan 2008 09:37:03 -0700
> > From: tec3.utah.edu
> > To: amber.scripps.edu
> > Subject: Re: AMBER: Has anyone seen a protein fall apart due to PBCs?
>
> >
> >
> > > I'm simulating with the AMBER FF99SB forcefield, and the tetrameric
> protein
> > > I've got seems to like to break into along the weaker of the two
> tetramer
> > > interfaces. To be sure, there are single point mutants of this protien
> known
> >
> > ...what pops to my mind is possible issues with equilibration at constant
> > pressure with positional restraints as this scales the positions of the
> > monomers (when NPSCAL=1) of both the real and reference coordinates...
> > If you initially solvated with LEaP, this tends to underestimate the
> > density so the system will compress slightly bringing the monomers closer
> > together if you run constant P with NTR=1 (restraints). When the
> > restraints are turned off, the monomers will slightly repulse.
> >
> > Of course, this assumes that you did constant P with restraints (which I
> > cannot tell from the post but is consistent with standard equilibration
> > protocols). If you search the AMBER reflector archives for belly or
> > restraints and my name, there are a number of posts that show how to hand
> > modify the prmtop to put all the protein monomers into a single molecule
> > (for pressure scaling) and it would be worth checking if this is the
> > culprit...
> >
> > [If it is not due to constant P w/ restraints, my next guess would be salt
> > and/or hydration at the interface and suggests prudence in carefully
> > equilibrating w/ restraints for a long time, ~1-5 ns]
> >
> > --tec3
> >
> > p.s. note that I do not think this would be due to periodicity artifacts;
> > despite the arguments of Hunenberger and Weber from your group, there is a
> > nice paper in JBSD by Villarreal and coworkers (JBSD23, 135 (2005)) that
> > suggests the artifacts in reality are minimal (< kT), as does nice work by
> > Bader & Chandler, Smith & Pettitt, ...
> >
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Received on Wed Jan 23 2008 - 06:07:29 PST
