AMBER Archive (2006)

Subject: AMBER: saltcon variable

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Thu Jul 20 2006 - 14:00:01 CDT

Dear all,

I am using Amber 9 to simulate a big dimeric protein which is highly charged (-41 in total). Bacause of the dimension of the system I am trying the implicit solven model GBSA. I found that the default salt concentration (saltcon) for Debye-Hukel screening is 0. I wonder if some salt effect modeling could be useful in treating such a charged system and if it could help to better simulate a water environment . If yes, what could be a reasonable salt concentration to use in the simulation? I found in some works on DNA that a 0.1 M value was used.

Thank you in advance

Stefano Pieraccini

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