Dear list,
I am calculating binding entropy of dna to protein using MMPBSA. In the literature, researchers truncate the system by deleting the protein residues further than 8 Å away from the ligand to reduce the computational cost. I tried to extract the corresponding residues' trajectory and parmtop, and they match well in chimera visualisation. But gave me the below error:
File "/home/tm/Downloads/amber16/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/home/tm/Downloads/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 "/home/tm/Downloads/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 104, in make_trajectories
traj.Strip(INPUT['ligand_mask'])
File "/home/tm/Downloads/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 646, in Strip
raise InternalError('Cannot pass no mask to Strip!')
InternalError: Cannot pass no mask to Strip!
The command and control file work well for the full complex. Do I have to use tleap to process the truncated complex and get the coordinates and parmtop file that can be recognised by amber?
Thanks,
Tammy
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Received on Thu Mar 10 2022 - 22:30:02 PST
