Hello,
What default PBradii have you defined??
Best Regards
On Tue, 6 Aug 2019 at 18:37, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Dear Amber Users,
>
>
> I did the 50ns MD simulation of protein-ligand complex
> system by using ff14SB force field for protein and glycam force field for
> ligand (sialic acid). From the output trjectories I am trying to calculate
> the MM-PBSA binding free erergy of this complex system. During the
> calculation i have the error as "CalcError:
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with prmtop
> comp.top!
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh" .
> In that following I am attaching the ligand pdb file and the output of the
> terminal. Help me to solve this error.
>
>
>
> MMPBSA.py -O -i mmpbsa.in -o 1.out -sp 1.prmtop -cp comp.top -rp prot.top
> -lp lig.top -y md1_50.nc
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> cpptraj found! Using /home/vit/Documents/amber16/bin/cpptraj
> Preparing trajectories for simulation...
> 1500 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning PB calculations with
> /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/home/vit/Documents/amber16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 433, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with
> prmtop comp.top!
> PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh
>
> Exiting. All files have been retained.
>
>
>
> Thanks in advance
> with regards
> R. A. Jeyaram
> Research scholar
> Vellore Institute of Technology
> Tamil Nadu, India.
>
>
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Received on Tue Aug 06 2019 - 07:00:02 PDT
