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
>
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>
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Received on Wed Mar 06 2013 - 13:00:05 PST
