[AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein

From: Ñî´¨ <junaid.hust.edu.cn>
Date: Mon, 21 Sep 2015 12:30:38 +0800 (GMT+08:00)

Dear Amber Users

I have simulated the complex using amber14 with GPU. I have got problem while running the MMPBSA.py . I have got this problem with several complexes.

I used this commond
MMPBSA.py -O -i mmpbsa_2b.in -o final.dat -sp com_solvated.top -cp com.top -rp rec.top -lp lig.top -y *.mdcrd

My input file is..

Input file for running PB and GB in serial
&general
   endframe=50, keep_files=2,
strip_mask=":WAT:CL-"Na+",
/
&gb
  igb=2, saltcon=0.100,
/
&pb
  istrng=0.100,
/

the error message said.....

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber14/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /opt/amber14/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Beginning PB calculations with /opt/amber14/bin/mmpbsa_py_energy
  calculating complex contribution...
  File "/opt/amber14/bin/MMPBSA.py", line 104, in <module>
    app.run_mmpbsa()
  File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 416, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber14/bin/mmpbsa_py_energy failed with prmtop com.top!
    PB Bomb in pb_aaradi(): No radius assigned for atom 11 CB 2C

Exiting. All files have been retained

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Received on Sun Sep 20 2015 - 21:30:03 PDT
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