[AMBER] Problem in MMPBSA analysis

From: 崔佳文 <cui_jw17.sioc.ac.cn>
Date: Wed, 9 Oct 2019 10:39:30 +0800 (GMT+08:00)


  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>
  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
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,




Shanghai Institution of Organic Chemistry, Chinese Academy of Science
AMBER mailing list
Received on Tue Oct 08 2019 - 20:00:02 PDT
Custom Search