Hello!
I'm performing MMPBSA analysis of iron-sulfur and heme-containing protein and having some problems.
The error massage is as follow:
Loading and checking parameter files for compatibility...
sander found! Using /opt/amber18/bin/sander
cpptraj found! Using /opt/amber18/bin/cpptraj
Preparing trajectories for simulation...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber18/bin/sander
calculating complex contribution...
bad atom type: M1
File "/opt/amber18/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /opt/amber18/bin/sander failed with prmtop cp.prmtop!
Exiting. All files have been retained.
I tried to replace the $AMBERHOME/src/sander/mdread2.F90 file with the new file containing following information:
else if (atype == 'M1') then
x(l165-1+i) = 1.386d0 + 1.4d0
x(l170-1+i) = 0.00000d0
x(l175-1+i) = 0.00000d0
x(l180-1+i) = 0.00000d0
x(l185-1+i) = 0.00000d0
But it doesn't work. I wonder what could I do to solve this problem.
Thanks for your time and consideration. I am looking forward to hearing from you!
Best regards,
——————————
Cui
(+86)17621824824
Shanghai Institution of Organic Chemistry, Chinese Academy of Science
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Received on Tue Oct 08 2019 - 20:00:02 PDT
