AMBER Archive (2007)

Subject: Re: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 24 2007 - 09:14:24 CST

On Tue, Jan 23, 2007, Ray Luo wrote:
>
> Unfortunately the parameters are assigned in the sander program, not by
> Leap.

That is only true for the surface area parameters. Radii for GB and PB
calculations should be assigned by LEaP, and be present in the prmtop file.

I've lost the details of this thread, but by turning off the "gbsa" parameter
in sander, or using the alternate surface area calculation in mm_pbsa, this
sort of calculation ought to be able to proceed.

...good luck....dac

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