On Fri, Jan 22, 2016 at 5:08 AM, Saikat Dutta chowdhury <
pbr322.dutta.gmail.com> wrote:
> Dear Amber Users,
> I have simulated a peptide in explicit solvent environment and saved the
> trajectory. Now I am interested in doing stability calculation and for this
> I am using MMPBSA.py.
>
> As I have only a solvated prmtop file, I stripped solvent information and
> created a prmtop file using following command.
>
> *ante-MMPBSA.py -p wt_box.prmtop -c dry_wt_box.prmtop -s :19-652*5
>
> Next I proceeded for stability calculation using both GB and PB models
> using following command.
>
> *MMPBSA.py -O -i mmpbsa.in <http://mmpbsa.in> -sp wt_box.prmtop -cp
> dry_wt_box.prmtop -y mdproduction1_wt_box.mdcrd*
>
> Stability calculation using GB model finished successfully but the
> calculation failed when I am using PB model.
>
>
>
> *The error message I got:------------------------------------*Loading and
> checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/saikat/ambertools14/bin/mmpbsa_py_energy
> cpptraj found! Using /home/saikat/ambertools14/bin/cpptraj
> Preparing trajectories for simulation...
> 20 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning PB calculations with
> /home/saikat/ambertools14/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/home/saikat/ambertools14/bin/MMPBSA.py", line 96, in <module>
> app.run_mmpbsa()
> File "/home/saikat/ambertools14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/home/saikat/ambertools14/bin/MMPBSA_mods/calculation.py", line 79,
> in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/home/saikat/ambertools14/bin/MMPBSA_mods/calculation.py", line
> 416, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /home/saikat/ambertools14/bin/mmpbsa_py_energy failed with
> prmtop dry_wt_box.prmtop!
>
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 171 CG C6
>
> Exiting. All files have been retained.
> *------------------------------------*
>
> Could anyone suggest why I am not able to use PB model for the calculation.
>
If you Google this error message (e.g., "
PB Bomb in pb_aaradi(): No radius assigned for atom
")
you should get a number of threads that will help you.
For instance, the first hit is this:
http://archive.ambermd.org/201303/0550.html
which is a reply to
http://archive.ambermd.org/201303/0549.html
More of the threads from the Google search give more details about what
went wrong.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 22 2016 - 05:00:04 PST
