I'm using AMBER11, But installed Amber Tools 12 as suggested by Jason
Swails<
https://plus.google.com/u/0/112944493094477727846?prsrc=4>
.
Thanks,
Saugata
On Wed, Mar 6, 2013 at 3:41 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Most likely you didn't patch the bugfixes if you are using Amber12 ...
>
> Ray
>
> On Wed, Mar 6, 2013 at 12:30 PM, Saugata Hazra <saugata.iitk.gmail.com>
> wrote:
> > Hi all,
> >
> > I'm calculating the binding energy of a protein-ligand interaction which
> > contains Protein, metal and ATP.
> > According to your help I have put the metal with the protein and ATP was
> > treated as a ligand.
> >
> > After that when I was trying to run, I got the following error message.
> >
> > *Beginning PB calculations with
> /home/saugata/amber12/bin/**mmpbsa_py_energy
> > calculating complex contribution...
> > CalcError: /home/saugata/amber12/bin/**mmpbsa_py_energy failed with
> prmtop
> > ba2291_atp_mg_vac.prmtop!
> > PB Bomb in pb_aaradi(): No radius assigned for atom 2369 O1G
> O3
> >
> > Exiting. All files have been retained.*
> >
> > After that, I have followed this link
> > http://archive.ambermd.org/201208/0074.html and added inp=1, radiopt=0
> into
> > the mmpbsa.in (attached with this mail)
> > But I'm still getting the same error message.
> > Please let me know if you could provide any help.
> >
> >
> >
> >
> > --
> >
> > *
> > *
> > Dr. Saugata Hazra
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
*Know me Know fun, no me no fun!!!*
Dr. Saugata Hazra
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Received on Wed Mar 06 2013 - 13:00:05 PST
