Hi all
My name is jong hui hong in Seoul Korea
while I run MD simulation and calculation of free energy by MMPBSA with MD simulation trajectory
I got the following error:
20 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/amber22/bin/mmpbsa_py_energy
calculating complex contribution...
File "/usr/local/amber22/bin/MMPBSA.py", line 100, in
app.run_mmpbsa()
File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 519, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /usr/local/amber22/bin/cpptraj failed with prmtop ../../prep/com.top!
mmpbsa run input file is following
Input parameters for running MM/PBSA
&general
startframe = 1,
endframe = 20,
interval = 1,
verbose = 2,
keep_files = 0,
/
&gb
igb = 5,
saltcon = 0.150,
/
I use use_sander=1 but ther result was same except that cpptraj was changed into sander
sander failed with prmtop ../../prep/com.top
what could be the problem?
Attached files are my MD simulation result
After uncompressing goto /3o9fA_K2D/traj_1/mmpbsa
and execute ./run_mmpbsa.sh then result can be reproduced
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Received on Thu Sep 19 2024 - 07:30:02 PDT
