If you google "PB Bomb in pb_aaradi(): No radius assigned for atom" you
will find a number of hits on the Amber mailing list that talk about the
lack of radii for certain (newer) force fields.
http://archive.ambermd.org/201208/0074.html is an example.
Good luck,
Jason
On Mon, Dec 3, 2012 at 2:40 PM, Rahul Banerjee <
rahul.banerjee.chemistry.msu.edu> wrote:
> I have done Amber12 simulation for a preotein-protein complex with
> explicit solvent. I have used FF12SB force field. Now I am trying to
> perform MMPBSA calculation with the following script:
> General MMPBSA.py input file
>
> &general
> startframe=1, endframe=100, interval=50, receptor_mask=:1-64,
> ligand_mask=:65-146,
> keep_files=0, verbose=1, strip_mask=:WAT:Na+,
> /
> &gb
> igb=5, saltcon=0.1,
> /
> &pb
> istrng=0.1, exdi=80, indi=1.0,
> inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
> fillratio=4, scale=2.0,
> linit=1000, prbrad=1.4, radiopt=1,
> /
>
> It returns with the following error:
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
> cpptraj found! Using /opt/software/Amber/12--Intel-12.1.2.273/bin/cpptraj
> Preparing trajectories for simulation...
> 2 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with
> /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
> failed with prmtop ../cplx_conf.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB
> 2C
>
> Exiting. All files have been retained.
>
> ATOM 14 is a Ser residue CB atoms. I am wondering why the program cannot
> recognize such a obvious atom type. Given topology file works fine with all
> other ptraj input or visualizing purposes.
>
> Please let me know if you have any clue or how to overcome this problem.
>
> With best regards,
> Rahul
> _______________________________________________
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> 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 Mon Dec 03 2012 - 12:00:02 PST
