AMBER Archive (2009)

Subject: [AMBER] implicit and explicit simulation: salt effect

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Jan 09 2009 - 21:03:35 CST

Dear Sir/Madam, I would like to study the salt effect for the binding of a neutral drug with DNA from 0M to 0.5 M of salt in a QUALITATIVE manner. It seems to me that I can do the GB simulation with salt effect considered. According to amber website, it seems to me that it is not a problem at all to do the simulation up to 0.2M salt. What about up to 0.5 M of salt for qualitative analysis? If I should only do the analysis with explicit solvent, how can I incorporate salt effects in the simulation? what is the command line should I used? Best regards, Cat

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