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

From: Jason Swails <>
Date: Thu, 4 Oct 2012 18:28:08 -0400

On Thu, Oct 4, 2012 at 6:20 PM, Sajeewa Pemasinghe <>wrote:

> 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
> range
> 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?

You need to use the command
set default pbradii bondi

in tleap. If you already have a topology file, you can set the radius set
using ParmEd directly, without having to go through tleap again. Open up
the prmtop in (you can run that command with no arguments and
choose your prmtop, or ), choose "changeRadii", and select bondi.

Note, I think that igb=8 is a significantly better GBn model, so that may
be worth using instead (this uses the mbondi3 radius set, which can be set
the same way).

See this page for details about using parmed:


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Oct 04 2012 - 15:30:03 PDT
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