Dear Amber user group
I encountered an error when I ran the MMPBSA calculation with amber 14.
I generated the topology files as inputs for MMPBSA using ante-MMPBSSA.py
ante-MMPBSA.py -p $Solvated_Complex --complex-prmtop Complex_nW.prmtop
--receptor-prmtop Protein.prmtop --ligand-prmtop Ligand.prmtop --strip-mask
":WAT:Na+" --receptor-mask ":1-473" --radii mbondi2
I ran the MMPBSA calculation with the following command.
MMPBSA.py.MPI -O -i PBSA.in -o Result_PBSA.dat -do Result_Decomposition.dat
-sp $Solvated_Complex -cp Complex_nW.prmtop -rp Protein.prmtop -lp
Ligand.prmtop -y 04equil.mdcrd
(By the way, why I can not receive reply directly from amber mail list? I
always checked the reply in the archive. How should I set the reply
settings? Thanks a lot!)
The error message I got as follows:
Error: # atoms in TRX file (0) does not match # atoms in parm
Complex_nW.prmtop (7176)
Error: Could not set up _MMPBSA_avgcomplex.pdb for reading.
Error: reference: Could not set up trajectory.
1 errors encountered reading input.
File "/lap/amber/14.0.12/bin/MMPBSA.py.MPI", line 104, in <module>
app.run_mmpbsa()
File
"/lap/amber/14.0.12/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/lap/amber/14.0.12/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/lap/amber/14.0.12/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 375, in run
Calculation.run(self, rank, stdout=self.output)
File
"/lap/amber/14.0.12/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /lap/amber/14.0.12/bin/cpptraj failed with prmtop
Complex_nW.prmtop!
Error occured on rank 18.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 18
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Received on Thu Oct 22 2015 - 15:00:03 PDT
