[AMBER] Need help with MMPBSA-per residue decomp

From: Yen Nguyen <ynguyen3.gmu.edu>
Date: Tue, 31 Aug 2021 02:45:54 +0000

Hello everyone,

This is my first time using amber, and I'm having a hard time trying to get the per-residue decomposition step to run successfully. I've been following this tutorial for MMPBSA on the amber website https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.php but had to make some modifications to make it work for me. I ran the production 4 times to get a total of 32 ns and used the last production run's mdcrd as the input for the MMPBSA step. I stripped the water and Na+ ions from the mdcrd file before using it for the decomp. I also had to choose the nobox option to avoid the box coordinates error in the mmpbsa calculation step. I had to modify my mmpbsa input file so many times to get the mmpbsa script from failing immediately when submitting to my school remote clusters to failing after running for 2 hours. This thread http://archive.ambermd.org/201912/0023.html said that explicitly defining the strip_mask, receptor_mask and ligand_mask solved the problem, but it did not in my case.

I also could not use the dry.prmtop file generated by tleap in the mmpbsa calculation, as it will immediately send the CalcError with prmtop error, so I've used ante-mmpbsa.py to generate the dry.prmtop file from the solvated.prmtop file. The executable was
ante-mmpbsa.py -p solvated.prmtop -c dry.prmtop -s :WAT:NA --radii mbondi2

My protein (1ids) does not have a ligand bound to it, and for my research purpose, my principle investigator said I only need to use the dry and solvated prmtop files for the decomp. So my mmpbsa executables were different from what they had in the tutorial

My executables

MMPBSA.py -O -i /scratch/ynguyen3/AMBER/SOD-project/mmpbsa-perres-decomp-1ids-noFe-792res-Na-waterstripped.in -o /groups/MPLAB/YNguyen/AMBER/SOD-project/Results/MMPBSA/mmpbsa-perres-decomp-1ids-noFe-792res-Na-waterstripped-nobox.dat -sp /scratch/ynguyen3/AMBER/SOD-project/1ids-noFe-solvated.prmtop -cp /scratch/ynguyen3/AMBER/SOD-project/1ids-noFe-dry-noNa-ante.prmtop -y /scratch/ynguyen3/AMBER/SOD-project/1ids-noFe-production-run1-4-intel-gpu-Na-water-stripped-nobox.mdcrd

Re: [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop from Qing Lv on 2019-12-04 (Amber Archive Dec 2019)<http://archive.ambermd.org/201912/0023.html>
From: Qing Lv <lvqingjiejie.163.com> Date: Thu, 5 Dec 2019 15:41:02 +0800 (CST) This problem was solved by explicitly defining the strip_mask, receptor_mask and ligand_mask. Thank you! Qing At 2019-12-05 12:32:05, "Qing Lv" <lvqingjiejie.163.com> wrote:

My mmpbsa.in file is as follow

   endframe=3200, verbose=1,
strip_mask= :WAT:NA, (If I don't add this the run will stop after 1 hr)
receptor_mask= :1-792,
  igb=5, saltcon=0.100,

I keep getting this same error (either immediately or after 1-2 hours of running)

*** Error in `/cm/shared/apps/amber/amber18-intel19u2/bin/sander': malloc(): memory corruption: 0x000000001b0215a0 ***
 File "/cm/shared/apps/amber/amber18-intel19u2/bin/MMPBSA.py", line 100, in <module>
  File "/cm/shared/apps/amber/amber18-intel19u2/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/cm/shared/apps/amber/amber18-intel19u2/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/cm/shared/apps/amber/amber18-intel19u2/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /cm/shared/apps/amber/amber18-intel19u2/bin/sander failed with prmtop /scratch/ynguyen3/AMBER/SOD-project/1ids-noFe-dry-noNa-ante.prmtop!

Exiting. All files have been retained.

The output text file that records the job process shows these:

Loading and checking parameter files for compatibility...
sander found! Using /cm/shared/apps/amber/amber18-intel19u2/bin/sander
cpptraj found! Using /cm/shared/apps/amber/amber18-intel19u2/bin/cpptraj
Preparing trajectories for simulation...
106 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /cm/shared/apps/amber/amber18-intel19u2/bin/sander
  calculating complex contribution...

Beginning PB calculations with /cm/shared/apps/amber/amber18-intel19u2/bin/sander
  calculating complex contribution...

It looks like the GB calculations were ok and the problem occurred at the PB calculations step? Could someone please help me with this? I don't know what else I need to change/try to make this work.

Any help would be greatly appreciated!

Thank you.


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Received on Mon Aug 30 2021 - 20:00:03 PDT
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