[AMBER] MMPBSA failed

From: Albert <mailmd2011.gmail.com>
Date: Wed, 03 Apr 2013 09:12:10 +0200

Hello:

  I preceeded my system prmtop file with ante-MMPBS by command:

ante-MMPBSA.py -p ../sys.prmtop -c ../npt4.trj -c
complex_unsolvated.prmtop -r receptor.prmtop -l ligand.prmtop -s ':WAT'
-n ':290'


then I submit to MMPBSA calculation, but it failed:


calculating receptor contribution...
   calculating ligand contribution...

Beginning PB calculations with
/cfs/klemming/scratch/s/shuguang/install/amber12/bin/mmpbsa_py_energy
   calculating complex contribution...
mmpbsa_py_energy failed with prmtop complex_unsolvated.prmtop!
     PB Bomb in pb_aaradi(): No radius assigned for atom 11 CB 2C

Exiting. All files have been retained.

thank you very much
Albert

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Received on Wed Apr 03 2013 - 00:30:04 PDT
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