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

From: Jason Swails <>
Date: Sat, 6 Jul 2013 00:10:22 -0400

On Fri, Jul 5, 2013 at 10:26 PM, Manikanthan Bhavaraju <> wrote:

> 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)

You can just use ParmEd to strip out the ions from your system without
having to go back through tleap. So something like this -p <your_prmtop> << EOF
loadRestrt <your_inpcrd>
strip :K+,Cl-
outparm noions.prmtop noions.inpcrd

That should generate a working prmtop along with a compatible restart file.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Jul 05 2013 - 21:30:02 PDT
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