If you go to the amber12 directory, what does:
./patch_amber.py --patch-level
return?
On Wed, Mar 6, 2013 at 3:50 PM, Saugata Hazra <saugata.iitk.gmail.com>wrote:
> 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
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> *Know me Know fun, no me no fun!!!*
> Dr. Saugata Hazra
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 06 2013 - 14:30:03 PST
