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
