Re: [AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation

From: Manikanthan Bhavaraju <>
Date: Fri, 5 Jul 2013 21:26:29 -0500

I have used TIP3P water model and also mentioned the monovalent parameter
command in the tleap while generating the topology files.
loadAmberParams frcmod.ionsjc_tip3p

After 80 ns of the simulation, the RMSd vs. time plot for the protein seems
to be stable. The crystallization of the counter ions is not effecting the
protein structure. Similarly, the volume and the density of the simulation
box are also consistent throughout the sampling process. Is this a valid
simulation protocol?

If not, I have removed all the counter ions and am trying to generate new
prmtop and inpcrd files. I am unable to generate them as mentioned in the
previous mail. Can you please tell me how to overcome the error ? (as
mentioned in my last mail)


On Fri, Jul 5, 2013 at 8:42 PM, Jason Swails <> wrote:

> On Fri, Jul 5, 2013 at 8:20 PM, Manikanthan Bhavaraju <
>> wrote:
> > Dear Amber developers,
> >
> > I have equilibrated and sampled a protein+lipid bilayer (POPC) system by
> > maintaining 0.1 M KCl concentration for 80ns using explicit solvent model
> > with Amber12 and ff99SB + lipid11 forcefields. The N-terminus (residues
> > 1-19) of the protein is anchored into the lipid bilayer. I have reimaged
> > the system using ptraj for every 10 ns. Upon inspecting the reimaged pdb
> > file in the VMD, I have observed that the majority of the K+ and Cl- ions
> > have formed crystals (in the form of FCC lattice). Starting from a few
> > crystal (smaller in size), by the end of 80ns of simulation the K+ Cl-
> ions
> > have aggregated to form a larger crystal. Is this a forcefield effect
> due
> > to ff99SB or Lipid11?
> >
> Probably neither. It's probably due to the ion parameters you used, and I
> didn't see that you mentioned which parameters you used. You should use
> the monovalent ion parameters designed for the specific water model you are
> using. For instance, if you are using TIP3P, you should put a command like
> loadAmberParams frcmod.ionsjc_tip3p
> or the equivalent one for TIP4Pew or SPCE. If you use the ff10 force field
> (which is equivalent to ff99SB for proteins), then using these new
> parameters for ions is enforced.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
AMBER mailing list
Received on Fri Jul 05 2013 - 19:30:03 PDT
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