Greeting sir,
when i was trying to run MMPBSA with a trajectory file from NAMD simulation it gave me this error:
Loading and checking parameter files for compatibility...CHAMBER prmtops found. Forcing use of sandersander found! Using /eb/software/AmberTools/17-intel-2017b/bin/sandercpptraj found! Using /eb/software/AmberTools/17-intel-2017b/bin/cpptrajPreparing trajectories for simulation.../eb/software/AmberTools/17-intel-2017b/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0 warn('Solvated topology %s has IFBOX == 0' % ifbox)1000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /eb/software/AmberTools/17-intel-2017b/bin/sander calculating complex contribution... File "/eb/software/AmberTools/17-intel-2017b/bin/MMPBSA.py", line 100, in <module> app.run_mmpbsa() File "/eb/software/AmberTools/17-intel-2017b/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/eb/software/AmberTools/17-intel-2017b/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/eb/software/AmberTools/17-intel-2017b/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run self.prmtop) + '\n\t'.join(error_list) + '\n')CalcError: /eb/software/AmberTools/17-intel-2017b/bin/sander failed with prmtop complex.prmtop!
the steps i made was as follow:
1- i used chamber in parmed to produce .prmtop and .inpcrd for the ligand, receptor, complex (without water), complex (solvated).
please notice that the solvated complex contained ions, however, the ligand, receptor, and complex (without water) dont have ions.
the command i used:
chamber -top *.rtf -str *.str -param *.prm -psf protein.psf -crd protein.pdb
.psf files were generated using CHARMM-GUI.
the .prm and .rtf and .str files were used from CHARMM-GUI output
2- then i used this command to run MMPBSA after changing directory to the folder containing the input file of MMPBSA and the files produced in step 1:
MMPBSA.py -O -i cemostat_pbsa.in -lp drug.prmtop -cp complex.prmtop -rp protein.prmtop -sp solvated.prmtop -y /lfs01/workdirs/cairo029u1/cemostat/charmm-gui-9154780042/namd/step5_production.dcd -o /lfs01/workdirs/cairo029u1/cemostat/charmm-gui-9154780042/namd/pps/FINAL_RESULTS_MMPBSA.dat
3- my input file was as follows:
&generalstartframe=1, interval=1,verbose=2, keep_files=0, full_traj=1/&pbfillratio=4.0/
i checked the number of atoms in each file and were as follows:
ligand: 52
receptor: 3521
complex (without water): 3521
complex (solvated): 34864
thank you for your help
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Received on Mon Jun 29 2020 - 15:30:04 PDT
