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
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Received on Sun Jun 17 2012 - 14:30:02 PDT
