On Wed, Mar 6, 2013 at 5:52 PM, Saugata Hazra <saugata.iitk.gmail.com>wrote:
> But I'm not using amber12, I'm using amber11. I'm sorry if I have
> misunderstood something.
>
But you are using MMPBSA.py from AmberTools 12. Ergo, you should have an
amber12 folder. Is this not the case?
>
> Saugata
>
> On Wed, Mar 6, 2013 at 5:12 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > 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
> > > > >
> > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
> > >
> > > *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
> >
>
>
>
> --
>
> *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
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Received on Wed Mar 06 2013 - 15:30:03 PST
