Hi Dan,
Thank you very much for this tutorial. It's definitely something that I'll
look into.
Have a great day,
Kamali
On Sun, Jun 17, 2012 at 9:32 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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
> シンディカラ ダニエル <http://goo.gl/fLAqx>
> 立命館大学 <http://www.ritsumei.jp/index_j.html>
> びわこ・くさつキャンパス<http://www.ritsumei.jp/accessmap/accessmap_bkc_j.html>
> クリエーション コア・２F・計算生命化学研究室（菊池研究室）
> 電話番号：077-561-2617 内線: 6841
> --
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>
>
>
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Received on Mon Jun 18 2012 - 05:30:04 PDT
