Re: [AMBER] pbsa

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 12 Sep 2011 09:00:20 -0700

Kirtana,

I think your reading is correct. Which release are you using?

All the best,
Ray

On Mon, Sep 12, 2011 at 8:56 AM, kirtana S <skirtana4.gmail.com> wrote:
> I am using pbsa to calculate solvent accessible surface area ,
>
> &cntrl
>  imin =5,
>  igb=10,
>  gbsa=2,
>  surften=1,
>
> &pb
>  epsout=80,
> &end
>
> It sends me an error as
> PB Bomb in pb_aaradii(): no radius assigned for atom 681 1fe
>
> I have a iron atom in my input file,in the manual it says if I set radiopt=0
> this should use the radii from
> prmtop file for both PB calculation and for NP calculation. Here I get
>
> PB Bomb in pb_read(): use of radii other than vdw sigma for
>                     np solvation dispersion/cavity is not supported!
>
> How can I set up the radii and calculate the solvent accessible surface area
> if I use radiopt =1
>
> I appreciate your suggestion.
>
> Thanks
> Kirtana
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Received on Mon Sep 12 2011 - 09:30:03 PDT
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