While I don't know how to solve the root problem of the addions2 command, I
can offer a possible workaround which will take a bit of computer time, but
may
give you better results.
In a manner similar to this tutorial:
http://sites.google.com/site/dansindhikara/Home/software/placement/tutorial,
you can
run a 3D-RISM simulation with water, K, and Cl on your system to get the 3D
distributions of each, then use the python
script in the tutorial to place explicit water, K, and Cl according to
their distributions. Not only will this get you a reasonable distribution
for K and Cl, but if there are any coordinating water and/or ions, it will
likely place them correctly.
The problem is that this will obviously take a lot more time than using
random placement in LEaP or ptraj. The 3D-RISM calculation on a large
system such as yours will likely take several hours. And it will take some
thought into preparing the solvent.
If you have no alternative and/or would like well-placed solvent/ion
locations you should consider this 3D-RISM approach.
-Dan
On Mon, Jun 18, 2012 at 6:28 AM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Dear Amber users,
>
> I'm trying to simulate an 800+ protein-RNA complex with a physiological
> concentration of 0.15 M KCl. During my first try to add ions and solvate
> the system, I added ions first and then solvated the system. However,
> during equilibration, I believe that this resulted in un-physiological
> "clumps" of KCl. As I saw in the AMBER mailing list archive, I tried to
> first solvate and then add ions using the addions2 command; however, my
> system was so big that Leap crashed. A similar situation occurred when I
> tried to use the ptraj randomizeions command. Does anyone know of a way
> that I can circumvent the clumping issue without crashing any programs?
>
> Thank you all very much, and have a great day,
>
> Kamali Sripathi
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara <http://goo.gl/fLAqx>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/> - Biwako Kusatsu
Campus <http://www.ritsumei.ac.jp/eng/html/about/abo_08.html/#kusatsu>
sindhikara.gmail.com
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Received on Sun Jun 17 2012 - 19:00:02 PDT
