AMBER Archive (2005)

Subject: Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: mingche Pan (panmingche_at_yahoo.com)
Date: Fri Dec 02 2005 - 12:09:28 CST

Were these differences observed with the same radii for Mg2+ and everything else, i.e. using the radii in the same prmtop file (for pbsa, this means using the radiopt=0)?

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  Sorry! I forgot to mention that for PB calculation, I used readiopt = 1, not 0. For each radius, I changed Both Born radii of Mg2+ in prmpot file and corresponding Mg2+ radius in the mdread.f file (for sander and pbsa). Did I do something wrong?
   
  Mingche

                
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