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 - 13:36:53 CST


Thank you, Ray! I guess that is the reason why all PB energies are the same. I will rerun the PB calculations. So when I used radiopt =1, where thoes parameters come from?
   
  Mingche

  

> 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?

Yes, you did it wrong. I suggest that you just use radiopt=0, i.e. use
the radii in the prmtop and change the radius of Mg2+ in the prmtop file.

Best,
Ray

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