Dear Amber user
I prepared the parameter topology files by using these
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
set default PBradii mbondi3
rec=loadpdb rec.pdb
loadamberprep cgmp.prepi
lig=loadpdb lig.pdb
gascomplex= combine {rec lig}
savepdb gascomplex gas.complex.pdb
saveamberparm gascomplex gas.complex.prmtop gas.complex.rst7
saveamberparm rec gas.receptor.prmtop gas.receptor.rst7
saveamberparm lig gas.ligand.prmtop gas.ligand.rst7
solvcomplex= combine {rec lig}
solvatebox solvcomplex TIP3PBOX 10.0
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0
savepdb solvcomplex wet.complex.pdb
charge solvcomplex
check solvcomplex
saveamberparm solvcomplex wet.complex.prmtop wet.complex.rst7
To do MMPBSA calculation
Per-residue GB and PB decomposition
&general
startframe=4501,
verbose=1, keep_files=0,
/
&gb
igb=5,
/
&pb
indi=2,
/
&decomp
idecomp=1,
dec_verbose=1,
/
the script I used is
#!/bin/bash
#SBATCH -p mid1
#SBATCH -A ayenenler
#SBATCH -J mmpbsa-cgmp
#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="cgmp.mdcrd"
/usr/bin/python2.7 $AMBERHOME/bin/MMPBSA.py -O -i
/truba/home/ayenenler/cyclase/mmpbsa-cgmp/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}
Following files were generated normally _MMPBSA_complex_gb.mdout.0
, _MMPBSA_complex_gb_surf.dat.0 , _MMPBSA_ligand_gb.mdout.0
, _MMPBSA_ligand_gb_surf.dat.0 , _MMPBSA_normal_traj_cpptraj.out
, _MMPBSA_receptor_gb.mdout.0 , _MMPBSA_receptor_gb_surf.dat.0 ,
but job stop during _MMPBSA_complex_pb.mdout.0 calculation the last line
of this file is
PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
and the error message display on mmpbsa.slurm.e2349751 is
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 416, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with
prmtop gas.complex.prmtop!
Exiting. All files have been retained.
Kindly guide me on how I can calculate the per residue energy
decomposition.
Kind Regards
On Mon, Jan 27, 2020 at 7:52 PM Rana Rehan Khalid <ray.binm.gmail.com>
wrote:
> Dear Sir
>
> 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 Tue Feb 04 2020 - 12:30:03 PST
