Hi amber users,
I am trying to calculate the binding energy between a ligand and a protein as a receptor using amber 16
The problem is that the receptor presents a Fe, and the coordinate sphere was parametrize using MCPB.py
This package assigned different atom types to the residues that constituted the coordinate sphere.
Then, when I am trying to calculate the mmpbsa this error comes out;
File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber16/bin/mmpbsa_py_energy failed with prmtop complex.top!
PB Bomb in pb_aaradi(): No radius assigned for atom 5826 NE2 Y1 -> This atom type is assigned to a residue of the coordinate sphere using MCPB.py
In order to solve this problem I have used the following keywords for the .PB calculation:
/
&pb
radiopt=0, inp=1, istrng=0.100,
cavity_surften=0.00542, cavity_offset=0.92,
/
It seems that works well, but how much affect to the mmpbsa binding energy, not recalculate the radius and use the ones that appear in the frcmod file?
if in the input file, I only ask for &pb using the MMPBSA.py ( amber16), the program started with the GB calculations as well?
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
The calculation is still running from yesterday afternoon. I don't have any error, only two warning sentence;
Warning: inp=1 was old default
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default value: 1.400
It's normal?
Thank you for your help in advanced
Sincerely
Anna Cebrián
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Received on Tue Apr 04 2017 - 06:30:03 PDT
