Dear all,
I get the following error when trying to decompose (polardecomp=1) the
solvation free energy from 3D-RISM in MMPBSA.py. The calculation actually
does a couple of frames and finally crashes.
----------------------------------------------------------------------------------------
Beginning 3D-RISM calculations with
/Users/campa/Amber/amber14/bin/rism3d.snglpnt
calculating complex contribution...
File "/Users/campa/Amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
269, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/Users/campa/Amber/amber14/bin/MMPBSA_mods/calculation.py", line
148, in run
self.prmtop))
CalcError: /Users/campa/Amber/amber14/bin/rism3d.snglpnt failed with prmtop
AB40.WT-WT.nowat.ildn.pdb.charmm.pdb.psfgen.pdb.amber.top!
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
----------------------------------------------------------------------------------------
with the simple following input:
------------------------------------------
&general
startframe=1,endframe=5000,interval=500,verbose=2, keep_files=2, netcdf=1,
full_traj=1, use_sander=0,
/
&rism
thermo="gf",polardecomp=1,rism_verbose=2,
/
------------------------------------------
The error appears either in serial or parallel calculations in MMPBSA.py
script of AMBER14. I use the ff99SB-ILDN forcefield and the topology file
was created originally with chamber but finally converted to "nornal" amber
topology file with cpptraj facility with the option "parmwrite out ...
nochamber". The same calculation without the option "polardecomp=1" ends
correctly. As it seems a problem related with settings of radii (CalcError)
I've tried to change the radii using parmed but the problem persists.
All comments welcome and thank you very much for the help,
Campa,
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Received on Thu Oct 22 2015 - 13:00:03 PDT
