[AMBER] MMGBSA error help

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 15 Oct 2021 13:50:37 +0000

Hello Amber users,

I am trying to setup a simple MMGBSA calculation on a PDK3 kinase ligand complex

So this is my command line I use
/usr/local/amber20/bin/MMPBSA.py -i mmpbsa.in -sp PDK3_tempol_solvated.prmtop -cp PDK3_tempol_gas.prmtop -rp PDK3_gas.prmtop -lp tempol_gas.prmtop -y PDK3_tempol_productionA.nc

Loading and checking parameter files for compatibility...
  File "/usr/local/amber20/bin/MMPBSA.py", line 98, in <module>
  File "/usr/local/amber20/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 610, in loadcheck_prmtops
    self.normal_system.Map(INPUT['receptor_mask'], INPUT['ligand_mask'])
  File "/usr/local/amber20/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 130, in Map
    "every atom in the complex topology!")
PrmtopError: provided receptor/ligand masks don't select every atom in the complex topology!
Exiting. All files have been retained.

My mmpbsa.in file looks like this:
  verbose = 1,
  keep_files = 1,
  endframe = 1250,
  interval = 1,
  strip_mask = ":WAT,Cl-,Na+",
  receptor_mask = ":1-388",
  debug_printlevel = 1,
  startframe = 1,
  netcdf = 0,
  ligand_mask = ":389",
  probe = 1.4,
  saltcon = 0.1,
  igb = 5,

Could someone pls help me on what I am doing wrong? My receptor is :1-388 residues and my ligand is residue no 389.
Not sure why it says there is mismatch.

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Received on Fri Oct 15 2021 - 07:00:02 PDT
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