Re: [AMBER] The problems with constant pH

From: Jason Swails <>
Date: Fri, 19 Nov 2010 10:13:50 -0500

Are the metal ions completely necessary for protein function? I say this
because constant pH only works in implicit solvent currently, and ions are
not well-treated in implicit solvent. If you can strip the metal ions, that
would probably help. I'm not sure what the "proper" way of treating
explicit metal ions in GB simulations is, if there even is one.

Also, there were a number of bug fixes released for constant pH simulations
that could give rise to this type of behavior. I'm not sure what version of
amber you're using, but bugfix.25 for amber10 and bugfix.49 for amber9.
Lastly, make sure you heat slowly. I suggest using nmropt restraints on the
TEMP0 variable while using positional restraints on the backbone atoms that
you soften up as the system equilibrates.

Good luck!

On Fri, Nov 19, 2010 at 2:36 AM, cwt <> wrote:

> Dear all,
> I am doing the constant pH simulations of Amber, for I can change the
> pH of system during the MD simulation. But I have met some problems
> which trouble me a lot.
> My system includes protein, ligand and three Mg2+ ions. When heating
> and equilibrating the system, which atoms should I restrain, all of
> them? After heat and equilibration, the conformation changed a lot
> and the RMSD increased to 10 above.At the first step in product MD,
> temperture increased to about 362K, I don't know why. At 480ps, the
> temperature turned to 400 above. And the simulation stopped at about
> 500ps, the error information is as followed:
> vlimit exceeded for step 259584; vmax = 1139.7184
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 10 1 3
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> Who can tell me what causes this and what should I modify about it?
> Thanks a lot!!
> Wen-ting Chu
> Jilin university, China
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Nov 19 2010 - 07:30:04 PST
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