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.
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Received on Thu Oct 22 2020 - 11:30:02 PDT
