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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Received on Sun Jan 11 2009 - 01:16:46 PST
