Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 11 Aug 2015 09:04:03 -0400

On Tue, Aug 11, 2015 at 8:09 AM, Sangita Kachhap <sangita.imtech.res.in>
wrote:

>
>
> I have taken default input just to check MMPBSA.py of AMBER14, following
> are the inputs.
>
> #input file for GB and PB calculation
> &general
> startframe=5
> endframe=100
> interval=5,
> verbose=2
> keep_files=0
> /
> &gb
> igb=5,
> saltcon=0.150,
> /
> &pb
> istrng=0.15
> fillratio=4.0
> /
>

‚ÄčTry setting inp=1 and radiopt=0 in the &pb section. The error you are
seeing likely results from using "optimized" radii with the inp=2 nonpolar
solvation free energy model. The more commonly used model for nonpolar
solvation energies is a simple SASA-based model specified by inp=1.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 11 2015 - 06:30:02 PDT
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