*Dear Amber experts,*
*
*
*Recently I want to run an entropy calculation. I always failed with the
following error:*
Line minimizer aborted: step at upper bound 0.0025465977
Line minimizer aborted: step at upper bound 0.0010051508
Line minimizer aborted: step at upper bound 0.0011997471
Line minimizer aborted: step at upper bound 0.019940301
Line minimizer aborted: step at upper bound 0.044056357
FATAL: allocation failure in vector()
CalcError: /opt/share/amber12/bin/mmpbsa_py_nabnmode failed with prmtop
complex.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
*The progress report is :*
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/share/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /opt/share/amber12/bin/cpptraj
mmpbsa_py_nabnmode found! Using /opt/share/amber12/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
10000 frames were processed by cpptraj for use in calculation.
15 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning GB calculations with /opt/share/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /opt/share/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning nmode calculations with /opt/share/amber12/bin/mmpbsa_py_nabnmode
calculating complex contribution...
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
*And my input script is :*
#! /bin/sh
#PBS -q eq9
#PBS -N Amber12
#PBS -l nodes=1:ppn=15
##PBS -l mem=2048MB
#PBS -e mpi_amber.err2b
#PBS -o mpi_amber.log2b
#PBS -m bea
#PBS -M ycqchemical.gmail.com
export PATH=/opt/share/Python-2.7.3/bin/:$PATH
export LD_LIBRARY=/opt/share/Python-2.7.3/lib:$LD_LIBRARY
export AMBERHOME=/opt/share/amber12
source /opt/share/etc/mpich-3.0.4.intel.sh
cd /scratch/s1007018600/analysis/PBSA/nmode/100/igb2/e1
pwd
date
pbs_mpirun $AMBERHOME/bin/MMPBSA.py.MPI -O -i nmodeigb2e1.in -o
nmodeigb2e1.dat -sp complex-sol.prmtop -cp complex.prmtop -rp
protein.prmtop -lp ligand.prmtop -y
/scratch/s1007018600/analysis/PBSA/salt/50/ligand-md1-3.binpos >
progress.log
date
What is the problem? How can I fix it? Please advise!
yours sincerely,
C.Q.Yan
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Received on Tue Jul 23 2013 - 06:00:02 PDT
