I checked with by setting "use_sander=1" in the &general section
file : _MMPBSA_complex_gb.mdout.0
error : FATAL: NATOM mismatch in coord and topology files
(reference
http://archive.ambermd.org/201407/0531.html)
FROM THE TERMINAL SCREEN
Loading and checking parameter files for compatibility...
sander found! Using /opt/amber16/bin/sander
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber16/bin/sander
calculating complex contribution...
File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
157, in run
self.prmtop))
CalcError: /opt/amber16/bin/sander failed with prmtop complex.prmtop!
Exiting. All files have been retained.
Thank you
On Thu, Dec 12, 2019 at 5:01 PM venkat <azbvenkat.gmail.com> wrote:
> Thank you for information sir,
>
> while removing the zero in the section DIHEDRAL_PERIODICITY of .prmtop
> file particular " 0.00000000E+00 "
>
> 1.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00
> 3.00000000E+00
> 3.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 2.00000000E+00 0.00000000E+00 2.00000000E+00
> 0.00000000E+00
> 2.00000000E+00 3.00000000E+00 0.00000000E+00 0.00000000E+00
> 2.00000000E+00
> 3.00000000E+00 3.00000000E+00 0.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
>
> made like this all parmtop solavted, complex, receptor
>
> 3.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 2.00000000E+00
> 2.00000000E+00 2.00000000E+00
> 2.00000000E+00 3.00000000E+00
> 3.00000000E+00 3.00000000E+00
> 2.00000000E+00 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
> 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
> 2.00000000E+00
>
> still facing error
>
> python2.7 /opt/amber16/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp FULL-AG13-ONE.top -cp complex.prmtop -rp
> receptor.prmtop -lp ligand.prmtop -y LAST5NS-FULL-AG13-ONE.dcd
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
> cpptraj found! Using /opt/amber16/bin/cpptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
> 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
> 157, in run
> self.prmtop))
> CalcError: */opt/amber16/bin/mmpbsa_py_energy failed with prmtop
> complex.prmtop!*
> Exiting. All files have been retained.
>
>
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Received on Thu Dec 12 2019 - 04:00:02 PST
