Dear Amber users,
I’m running MM-PBSA calculations of the binding affinity between a small molecule ligand and a complex formed by a protein, DNA and a Mg2+ ion with mmpbsa.py. All the elements of the complex interact with the small molecule and therefore contribute to its binding affinity.
When running mmpbsa.py with previously generated trajectories of the solvated complex, including &pb, &nmode and &decomp calculations, and calling for the input file with the following command:
/MMPBSA.py -O -i 3_Input_File_MMPBSA.in -o FINAL_RESULTS_MMPBSA.dat -sp Complex_solv.prmtop -cp Complex_dry.prmtop -rp Receptor.prmtop -lp Ligand.prmtop -y 5_Prod1.nc 5_Prod2.nc 5_Prod3.nc 5_Prod4.nc -do Final_Decomposition_MMPBSA.dat -eo Energy.csv -deo Energy_decomposition.csv
an error arises. The output of the program is:
/Users/da1712/Documents/1_Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py:606: UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
sander found! Using /Users/da1712/Documents/1_Programs/amber16/bin/sander
cpptraj found! Using /Users/da1712/Documents/1_Programs/amber16/bin/cpptraj
mmpbsa_py_nabnmode found! Using /Users/da1712/Documents/1_Programs/amber16/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
Error: In _MMPBSA_receptor.mdcrd.0, expect only 3 or 6 box coords, got 5
Error: Box line=[ 72.715 83.042 69.155 9.811 99.619
]
Error: Could not set up '_MMPBSA_receptor.mdcrd.0' for reading.
Error: Could not set up input trajectory '_MMPBSA_receptor.mdcrd.0'.
Error: Error(s) occurred during execution.
File "/Users/da1712/Documents/1_Programs/amber16/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/Users/da1712/Documents/1_Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File "/Users/da1712/Documents/1_Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 242, in make_trajectories
(trj_suffix, i) for i in range(size)], cpptraj)
File "/Users/da1712/Documents/1_Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
self.Query()
File "/Users/da1712/Documents/1_Programs/amber16/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: /Users/da1712/Documents/1_Programs/amber16/bin/cpptraj failed when querying _MMPBSA_receptor.mdcrd.0
Exiting. All files have been retained.
I wonder if you could help me elucidating what the problem might be. I read a previous post on the topic (
http://archive.ambermd.org/201306/0241.html ) that mentions that this could be due to the fact that the number of atoms in the prmtop doesn’t match the number of atoms in the trajectory. However, when using UCSF Chimera to visualize the trajectories this doesn’t appear to be the issue as the trajectory is loaded.
Any help will be welcomed. Many thanks.
Best wishes,
Diego
---------------------------------------------
Diego Alonso-Martinez – PhD Student
Biomolecular Mass Spectrometry and Computational Proteomics Group (BMSCPG)
Department of Chemical Engineering
Imperial College London (UK)
London SW7 2AZ
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Received on Mon Nov 13 2017 - 06:30:06 PST
