Dear Amber users
I am performing 3drism (first time) for energy calculation of a
protein-protein system.
input file
Input file for running PB and GB
&general
startframe=1,
endframe=100,
receptor_mask=":1-344",
ligand_mask=":345-498",
strip_mask=:WAT,
verbose=1,
entropy=0
/
&rism
polardecomp=0, thermo="std",
/
using command
mpirun -np 32 MMPBSA.py.MPI -O -i mmpbsa-rism.in -o
FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp t.top -cp
enz-lig.top -rp enz.top -lp lig.top -y c96-100.mdcrd > progress.log 2>&1
with following error message
Loading and checking parameter files for compatibility...
rism3d.snglpnt found! Using /opt/amber/amber14/bin/rism3d.snglpnt
cpptraj found! Using /opt/amber/amber14/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning 3D-RISM calculations with /opt/amber/amber14/bin/rism3d.snglpnt
calculating complex contribution...
File "/opt/amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/opt/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber/amber14/bin/MMPBSA_mods/calculation.py", line 269, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/opt/amber/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /opt/amber/amber14/bin/rism3d.snglpnt failed with prmtop lig.top!
Error occured on rank 29.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 29 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.
--------------------------------------------------------------------------
I have tried to build the topology files again but still shows the same
error over and over again.
Please help me to solve this problem.
Thanks in advance!
--
Vertika Gautam
Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya
*e-mail address: vartikapisces.gmail.com
<vartikapisces.gmail.com>
vartikapisces.hotmail.com <vartikapisces.hotmail.com>
01112294191*
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Received on Mon Apr 24 2017 - 02:00:02 PDT
