AMBER Archive (2008)

Subject: RE: AMBER: Has anyone seen a protein fall apart due to PBCs?

From: Irene Newhouse (
Date: Tue Jan 22 2008 - 11:28:44 CST

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:> To:> 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, ...> -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to> To unsubscribe, send "unsubscribe amber" to
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