[AMBER] MMPBSA

From: Farial Tavakoli <faryal.tavakoli.gmail.com>
Date: Fri, 14 Dec 2018 18:56:48 +0330

Dear all

I am new user in AMBER and need to simulate my complex including a protein
and a peptide with 2 phosphotyrosine residues using AMBER. I didnt install
AMBER, so the topology and coordinate files were generated using
ambertools18 according the scripts in amber 2018 manual,
source Leaprc.phosaa10
source oldff/ff99SB
source leaprc.water.tip3p
ligand = loadPDB ligand.pdb
receptor = loadPDB receptor.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm ligand ligand.top ligand.crd
saveAmberParm receptor receptor.top receptor.crd
saveAmberParm complex complex.top complex.crd
solvateOct complex TIP3PBOX 10.0
addions complex Na+ 11.00
saveAmberParm complex complex_solvated.top complex_solvated.crd
quit
Then I minimized and simulated the complex using all input files in " Molecular
Mechanics with a Poisson‚ÄźBoltzmann/Surface Area solvent: MM-PBSA
<http://ambermd.org/tutorials/advanced/tutorial3/index.htm>" in
AMBERtools18. To calculate the binding free energy using mmpbsa I used the
command and input file in the manual :
mpirun -np 2 MMPBSA.py.MPI -O -i mmpbsa.in -sp complex_solvated.top -cp
complex.top -rp receptor.top -lp ligand.top -y traj.crd

&general
startframe=1, endframe=10, interval=1,
verbose=2, keep_files=0,
/
&pb
istrng=0.15, fillratio=4.0
/

but faced to this error:

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/home/vaio/Downloads/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /home/vaio/Downloads/amber18/bin/cpptraj
Preparing trajectories for simulation...
10 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning PB calculations with
/home/vaio/Downloads/amber18/bin/mmpbsa_py_energy
  calculating complex contribution...
  File "/home/vaio/Downloads/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
    app.run_mmpbsa()
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
  File "/home/vaio/Downloads/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
    app.run_mmpbsa()
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
    self.calc_list.run(rank, self.stdout)
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
  File "/home/vaio/Downloads/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
  File "/home/vaio/Downloads/amber18/bin/MMPBSA.py.MPI", line 100, in
<module>
    app.run_mmpbsa()
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
    app.run_mmpbsa()
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
    self.calc_list.run(rank, self.stdout)
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File
"/home/vaio/Downloads/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 433, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/vaio/Downloads/amber18/bin/mmpbsa_py_energy failed with
prmtop complex.top!
    PB Bomb in pb_aaradi(): No radius assigned for atom 5255 OH OV
Error occured on rank 2.
.
.
.
Exiting. All files have been retained.

I searched google for this error and found this solution:
add inp=1 and radiopt=0 parameters to input file
but I faced this error this time:

Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: cavity_surften=0.0378 not recomended for inp=1, switching to inp=1
default value:0.005
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
CalcError: /home/vaio/Downloads/amber18/bin/mmpbsa_py_energy failed with
prmtop complex.top!

and when I added cavity_offset=0.00, cavity_surften=0.005 and sprob=1.40 to
the &pb part of the input file , faced to this error:

InputError: Unknown variable sprob in &pb

I dont know where the problem is? Is it possible that it is because of 2
phosphotyrosine residues in my ligand? I know there are some solutions in
google about this problem and I used them to solve that but The problem has
not yet been solved.
I would be reaaly appreciarlted it if anyone can help me.

best regards
Farial
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Received on Fri Dec 14 2018 - 07:30:02 PST
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