Dear Amber Users
I want to do MMPBSA energy calculation but every time simulation stops with
these error msg. Kindly help me.
mmpbsa.in
Per-residue GB and PB decomposition
&general
verbose=1, keep_files=0,
/
&gb
igb=8,
/
&pb
indi=2,
/
&decomp
idecomp=1,
dec_verbose=1,
/
///////////////////////mmpbsa.slurm///////////////////////////
#!/bin/bash
#SBATCH -p mid1
#SBATCH -A ayenenler
#SBATCH -J mmpbsa-gtp
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --time=04-00:00:00
#SBATCH --output=slurm-%j.out
#SBATCH --error=slurm-%j.err
echo "SLURM_NODELIST $SLURM_NODELIST"
echo "NUMBER OF CORES $SLURM_NTASKS"
source /truba/sw/centos6.4/app/amber/amber14/amber.sh
module load centos6.4-intel/lib/openmpi/1.6.5-gcc
export AMBERHOME="/truba/sw/centos6.4/app/amber/amber14"
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
#Define topology files
solv_prmtop="wet.complex.prmtop"
complex_prmtop="gas.complex.prmtop"
receptor_prmtop="gas.receptor.prmtop"
ligand_prmtop="gas.ligand.prmtop"
trajectory="gtp.mdcrd"
/usr/bin/python2.7 $AMBERHOME/bin/MMPBSA.py -O -i
/truba/home/ayenenler/cyclase/mmpbsa-gtp/1/mmpbsa.in -o mmpbsa.results.dat
-eo mmpbsa.per-fram.dat -sp ${solv_prmtop} -cp ${complex_prmtop} -rp
${receptor_prmtop} -lp ${ligand_prmtop} -y ${trajectory}
//////////////////////////////////////////////////////ERROR/////////////////////////////////////////////////
File "/truba/sw/centos6.4/app/amber/amber14/bin/MMPBSA.py", line 96, in
<module>
app.run_mmpbsa()
File "/truba/sw/centos6.4/app/amber/amber14/bin/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/truba/sw/centos6.4/app/amber/amber14/bin/MMPBSA_mods/calculation.py",
line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/truba/sw/centos6.4/app/amber/amber14/bin/MMPBSA_mods/calculation.py",
line 148, in run
self.prmtop))
CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with
prmtop gas.complex.prmtop!
Exiting. All files have been retained.
////////////////////////////////////////////////////////OUT////////////////////////////////////////////////////////////
SLURM_NODELIST levrek160
NUMBER OF CORES 4
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
5000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/truba/sw/centos6.4/app/amber/amber14/bin/sander
calculating complex contribution...
sander found! Using /truba/sw/centos6.4/app/amber/amber14/bin/sander
cpptraj found! Using /truba/sw/centos6.4/app/amber/amber14/bin/cpptraj
Finished Production on .4 20:04:54 +03 2020
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Looking forward to the response.
Cheers,
Rehan
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Received on Mon Jan 27 2020 - 09:00:02 PST
