[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
line1420,
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>

    app.run_mmpbsa()

  File
"/Users/subha/Downloads/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa

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

  File
"/Users/subha/Downloads/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run

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

  File
"/Users/subha/Downloads/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 478, in run

    self.prmtop))

CalcError: /Users/subha/Downloads/amber16/bin/cpptraj failed with prmtop
ligand.top!

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?
 ----------
//mm.in//
-----------
&general
startframe=1, endframe=2, interval=1,
verbose=3, keep_files=2,
/
&gb
igb=2, saltcon=0.150,
/
&decomp
idecomp=2, dec_verbose=3,
/
-----------

Thanks and Best Regards,
Subha
-- 
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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