AMBER Archive (2009)

Subject: [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sat Aug 15 2009 - 23:18:28 CDT

Dear Sir/Madam,

 

Should I do neutralize the charges in DNA-protein complex with Na+ or Mg2+ (before adding solvent) when we generate the prmtop or inpcrd files? I found Na+ was used in the tutorial, but some paper used Mg2+, why?

 

Best regards,

 

Cat

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