[AMBER] Modifying mdread2.F90 for bad atom type: "I" MMPBSA error

From: Subha Kalyaanamoorthy <kalyaana.ualberta.ca>
Date: Fri, 11 Jan 2019 11:29:45 -0700

Hi There,

Running MMPBSA.py for a ligand-protein complex with an Iodine atom (present
in the ligand) gave a bad atom type error. Looking through the mailing
list, I modified the mdread2.F90 and added the following lines after
else if (atype == 'I') then
               x(l165-1+i) = 1.98d0 + 1.4d0
and also added the below lines after line 1497 and 1560,
else if (atomicnumber .eq. 53) then
               x(l165-1+i) = 1.98d0 + 1.4d0
I recompiled the package in serial and ran the MMPBSA.py script.
Although, I don't get the bad atom type error, the calculations stop at the
ligand contribution as shown below.

Loading and checking parameter files for compatibility...

CHAMBER prmtops found. Forcing use of sander

sander found! Using /Users/subha/Downloads/amber16/bin/sander

cpptraj found! Using /Users/subha/Downloads/amber16/bin/cpptraj

Preparing trajectories for simulation...

2 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /Users/subha/Downloads/amber16/bin/sander

  calculating complex contribution...

  calculating receptor contribution...

  calculating ligand contribution...

  File "/Users/subha/Downloads/amber16/bin/MMPBSA.py", line 100, in <module>


line 218, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

line 82, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

line 478, in run


CalcError: /Users/subha/Downloads/amber16/bin/cpptraj failed with prmtop

Exiting. All files have been retained.
I tried with igb= 2 and 5 and it gave me the same result. The
_MMPBSA_ligand_gb.mdout.0 seems to have no problem. Could somebody help me
find the problem here?
startframe=1, endframe=2, interval=1,
verbose=3, keep_files=2,
igb=2, saltcon=0.150,
idecomp=2, dec_verbose=3,

Thanks and Best Regards,
Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.

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Received on Fri Jan 11 2019 - 11:00:02 PST
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