Hello King,
In general, the instructions for what you want to do are here:
http://ambermd.org/tutorials/advanced/tutorial8/loop4.htm
Whether you use solvateBox or solvateOct or some other method to add
your water box, you will need to take note of the volume of the
resulting water box. As you can see on the tutorial page, it prints out
a volume in cubic Angstroms.
You will then need to convert from mM to particles per unit cell. I
trust you will find this a simple calculation.
If the number of particles per unit cell is N, then:
* Number of chloride ions to add = N
* Number of sodium ions to add = N + 12
Does that make sense?
Regards,
Ben Roberts
On Wed, 2021-11-10 at 22:11 -0800, King Wu wrote:
> Hello AMBER,
>
> My system has -12 charge, and I wonder how I can make my system with ion
> concentration 150mM NaCl in the system preparation using Tleap?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 10 2021 - 23:00:02 PST
