I'm asking MJ to take a look ...
Ray
---------- Forwarded message ----------
From: kirtana S <skirtana4.gmail.com>
Date: Mon, Sep 12, 2011 at 9:05 AM
Subject: Re: [AMBER] pbsa
To: AMBER Mailing List <amber.ambermd.org>
Thanks for your reply
I am using amber10. bin/pbsa for my calculations
On Mon, Sep 12, 2011 at 12:00 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> 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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> >
>
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Received on Mon Sep 12 2011 - 10:30:04 PDT
