[AMBER] mmpbsa

From: Farial Tavakoli <faryal.tavakoli.gmail.com>
Date: Thu, 13 Dec 2018 20:29:04 +0330

Dear all

I am new AMBER user and need to simulate my complex including a protein and
a peptide with 2 phosphotyrosine residues, I didnt install AMBER and so the
topology and coordinate files were generated using ambertools18 according
the scripts in amber 2018 manual, but since, I had to use ffphosaa10 to
create topology file for the peptide, so I used ff99SB instead of ff14SB in
manual:
source leaprc.protein.ff99SB
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=5, endframe=100, interval=5,
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 4R3R-MIG6pYpY.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.
    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 4R3R-MIG6pYpY.top!
    PB Bomb in pb_aaradi(): No radius assigned for atom 5255 OH OV

Error occured on rank 1.
Exiting. All files have been retained.
    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 4R3R-MIG6pYpY.top!
    PB Bomb in pb_aaradi(): No radius assigned for atom 5255 OH OV

Error occured on rank 3.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
    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 4R3R-MIG6pYpY.top!
    PB Bomb in pb_aaradi(): No radius assigned for atom 5255 OH OV

Error occured on rank 0.
Exiting. All files have been retained.
[vaio-VPCEA42EG:02566] 3 more processes have sent help message
help-mpi-api.txt / mpi-abort
[vaio-VPCEA42EG:02566] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help / error messages
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: 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 4R3R-MIG6pYpY.top!
and when I added cavity_seoff=0.00, cavity_surften=0.00 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?
Is there anyone who can help me?

best regards
Farial
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Received on Thu Dec 13 2018 - 09:00:03 PST
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