Dear Jason,
Very thanks for your answers.
I have 9 protein-ligand complexes.
The errors in my previous email were related to number 1 complex.
I did GB and quasi-harmonic calculations for number 2 complex and
I encountered with following error:
Running calculations on normal system...
Beginning GB calculations with
/share/apps/amber/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning quasi-harmonic calculations with
/share/apps/amber/amber14/bin/cpptraj
Error: # atoms in TRX file (0) does not match # atoms in parm comp.prmtop
(5042)
Error: Could not set up _MMPBSA_avgcomplex.pdb for reading.
Error: reference: Could not set up trajectory.
1 errors encountered reading input.
File "/share/apps/amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/share/apps/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79,
in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
363, in run
Calculation.run(self, rank, stdout=self.output)
File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
148, in run
self.prmtop))
CalcError: /share/apps/amber/amber14/bin/cpptraj failed with prmtop
comp.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
I used following command line:
mpirun -np 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmgbsa_qh.in -o
mmgbsa_qh.dat -sp
comp_sol.prmtop -cp comp.prmtop -rp pr.prmtop -lp lig_h.prmtop -y
autoimaged.binpos &
I did GB calculation without any problem. I want to obtain entropy
proportion.
What is your suggestion?
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Received on Tue Dec 01 2015 - 11:30:03 PST
