Re: [AMBER] Adding Ions.

From: Hugh Heldenbrand <>
Date: Wed, 30 Jun 2010 13:27:04 -0500

For my simulations I use ptraj's randomizeions function to achieve what
you are asking for (see page 120 of the AmberTools v1.4 Manual).

-Hugh Heldenbrand
Graduate Student, University of Minnesota

Ajay Ummat wrote:
> I want to add 150mM Na+ Cl- ions in my system. I used the command: addions x
> Na+ 91 Cl- 96 (as my system had +ve 5 charge and I needed 96 each of Na+ and
> Cl-). When I visualize the result of adding ions, leap has added all the
> ions only on one particular side of the protein. This certainly seems
> unreasonable. Can anyone suggest me a way of uniformly distributing the ions
> around the protein. When I say uniformly I mean to consider eletrostatics of
> the distribution. A skewed distribution of charges would make my production
> run unrealistic and unreliable. Thanks in advance.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Jun 30 2010 - 12:00:04 PDT
Custom Search