Hi, All,
I had some issues when I ran MMPBSA.py to calculate the free binding energy
of two proteins.
One of the protein (receptor) has a Mg2+ ion coordinated with residues (D
and S) inside the protein. The ligand protein comes and binds to the
receptor by coordinating with the Mg2+ ion by a E residue. Therefore, in
the complex, the two proteins are connected by one Mg2+ ion so that Mg2+
ion is crucial for this binding.
However, when I included Mg2+ in the receptor mask when running MMPBSA.py,
I got issues. The error information I got is as below:
Loading and checking parameter files for compatibility...
sander found! Using /home/jz347/Amber17Pure/bin/sander
cpptraj found! Using /home/jz347/Amber17Pure/bin/cpptraj
mmpbsa_py_nabnmode found! Using
/home/jz347/Amber17Pure/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 7
Error: Box line=[ 69.184 25.640 44.865 69.883 24.944 46.082 70.198
]
Error: Could not set up '_MMPBSA_complex.mdcrd.0' for reading.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
Error: Error(s) occurred during execution.
File "/home/jz347/Amber17Pure/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File
"/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File
"/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
line 216, in make_trajectories
(trj_suffix, i) for i in range(size)], cpptraj)
File
"/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
line 467, in __init__
self.Query()
File
"/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
line 602, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /home/jz347/Amber17Pure/bin/cpptraj failed when querying
_MMPBSA_complex.mdcrd.0
Exiting. All files have been retained.
I'm sure that the ligand and receptor mask indexes are correct. I loaded
the _MMPBSA_complex.mdcrd.0 file in VMD and found that all structures were
messed up. Then I counted the atom in one snapshot of mdcrd file and found
that there is one residue less than my specified mask. I think the missing
atom must be the Mg ion.
Then I ran another MMPBSA.py and did not include Mg in the receptor mask.
This time MMPBSA.py ran successfully. It seems that the Mg atom was causing
the box coords error, although I don't know why. However, in this
situation, the binding free energy calculated was positive. I think it
should be due to the repulsion of two proteins when the crucial Mg ion is
missing.
My question is: Is there a way that I can include the Mg ion in the
receptor mask so that I can calculate the real binding free energy?
Best,
Jie
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Received on Tue Feb 27 2018 - 14:30:02 PST
