Re: [AMBER] error during the calculation of MMPBSA

From: <>
Date: Tue, 06 Aug 2019 21:50:54 +0800

   If you're using an older version, such as amber 16, please add radiopt=0 in
   your PB keyword section of the input file.
   But please update to the latest version ... it's free.
   All the best,
   Ray Luo, Ph.D.

   -------- Original Message --------
   Subject: [AMBER] error during the calculation of MMPBSA
   From: Jeyaram R A

     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!
         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. -O -i -o 1.out -sp 1.prmtop -cp -rp
     -lp -y
     Loading and checking parameter files for compatibility...
     mmpbsa_py_energy found! Using
     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
       calculating complex contribution...
       File "/home/vit/Documents/amber16/bin/", line 100, in <module>
     py", line 218, in run_mmpbsa, self.stdout)
     "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calcu", line 82, in run, stdout=stdout, stderr=stderr)
     "/home/vit/Documents/amber16/lib/python2.7/site-packages/MMPBSA_mods/calcu", line 433, in run
         self.prmtop) + '\n\t'.join(error_list) + '\n')
     CalcError: /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with
         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
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