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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Thu, Oct 22, 2020 at 11:10 AM divyabharathi korlepara <divyabharathik938.gmail.com> wrote: > > Dear Amber users, > I am trying to calculate binding affinity using MMPBSA calculation > for protein-ligand system. I want to include one explicit water molecules > in the calculations. > > For that, I created topology file for ligand, protein+1 water molecule > using following lines. > > > 1. From fully solvated topology file I removed the counter ions as > follows > > $ cpptraj > > > > > > *parm ../../file_preparation/complex_solvated.prmtoptrajin sim1.dcdstrip > :Na+ outprefix striptrajout strip.dcdrunexit* > > 2. After removing the counter ions, I topology file for > protein+ligand+(one closest water molecule near ligand) > > $ cpptraj > > > > > > > *parm ./strip.complex_solvated.prmtoptrajin strip.dcdclosest 1 :LIG > outprefix complex_1_wattrajout complex_1_water.mdcrdtrajout > complex_1_water.pdbrunexit* > > 3. Using below lines I am creating topology file for protein+one > water molecule > > $ cpptraj > > > > > *parm ./complex_1_wat.strip.complex_solvated.prmtoptrajin > complex_1_water.mdcrdstrip :LIG outprefix protein_1_waterrunexit* > > 4. I created the topology file for ligand molecule. > > $ cpptraj > > > > > *parm ./complex_1_wat.strip.complex_solvated.prmtoptrajin > complex_1_water.mdcrdstrip !:LIG outprefix ligandrunexit* > > Finally, I am trying to run MMPBSA.py (from amber18) as follows: > > *MMPBSA.py -O -i mmpbsa.in <http://mmpbsa.in> -o FINAL_RESULTS.dat -cp > complex_1_wat.strip.complex_solvated.prmtop -rp > protein_1_water.complex_1_wat.strip.complex_solvated.prmtop -lp > ligand.complex_1_wat.strip.complex_solvated.prmtop -y complex_1_water.pdb* > > *I got the following error:* > > Loading and checking parameter files for compatibility... > mmpbsa_py_energy found! Using /usr/local/apps/amber18/bin/mmpbsa_py_energy > cpptraj found! Using /usr/local/apps/amber18/bin/cpptraj > Preparing trajectories for simulation... > Error: Could not initialize action [rmsd] > 1 errors encountered reading input. > Error: Error(s) occurred during execution. > File "/usr/local/apps/amber18/bin/MMPBSA.py", line 99, in <module> > app.file_setup() > File > "/usr/local/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", > line 156, in file_setup > self.mpi_size, str(external_progs['cpptraj']), self.pre) > File > "/usr/local/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", > line 134, in make_trajectories > traj.Run(pre + 'normal_traj_cpptraj.out') > File > "/usr/local/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", > line 687, in Run > raise TrajError('Error running %s' % self.program) > AttributeError: 'Trajectory' object has no attribute 'program' > Exiting. All files have been retained. > > Can someone please help me to identify the error. > > Thanks, > Divya. > > Dr. Divya Bharathi, > Post Doctoral Fellow, > IIIT > Hyderabad-500032. > INDIA. > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Oct 30 2020 - 08:30:02 PDT