Hi
you can use parmed.py to assign atoms taht are not identified .
then it will work.
i had similar problem and got PB Delta G.1000 kacal. .inp=1, radiopt=0
so i changed inp=2, radiopt=1
and
using parmed.py I changed my complex-nowat.top, receptor_nowat.top and
ligand_nowat.top files. for CB, CD, CD1, CD2, CG, CG1, CG2, CE
e.g of how to to use pamed.py
/analysis/CRD$ parmed.py
armEd: a Parameter file Editor
Choose an Amber Topology file to load: T_C98ligand.top
Loaded Amber topology file T_C98ligand.top
Reading input from STDIN...
> change AMBER_ATOM_TYPE .CB C
>outparm new_corrected.top
On Tue, Dec 4, 2012 at 1:25 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > _______________________________________________
> > 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
>
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Received on Thu Dec 27 2012 - 04:00:02 PST
