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

From: mingche Pan <>
Date: Fri, 2 Dec 2005 11:36:53 -0800 (PST)

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?


> 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.


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Received on Fri Dec 02 2005 - 19:53:00 PST
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