[AMBER] How do I generate prmtop files with bondi radii?

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, 4 Oct 2012 18:20:36 -0400

Hi all,

I am running MD using generalized Born solvation model. While I was running
my minimization I go this error message.

 Atom 109 has radius 0.800000000000000 outside of allowed
 of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi radii.

The atom number 109 is a gamma hydrogen of the amino acid serine. Could
anyone please tell me how to generate prmtop files using bondi radii as has
been suggested?

Thank you

Sajeewa Dewage
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Received on Thu Oct 04 2012 - 15:30:02 PDT
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