Dear all,
When I run MMGB/PBSA wiht the following input, I got the following error
message at some point. But when I change the interval to 4 or 5 the
calculation runs fine with out any problem. I got same error message if I
go to 2. ( I have not done 1). The error says there is problem in topology
file but it is little bit weird that the same topology file is good for the
other cases but not when you change the interval. I would really appreciate
if you could give your opinion on whats going on here.
&general
startframe=500, endframe=3500, interval=3,
verbose=2, keep_files=2, strip_mask=':WAT,CL',
/
&gb
igb=8, saltcon=0.150,
/
&pb
inp=1, radiopt=0, istrng=0.15, fillratio=4.0
/
Error message:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
cpptraj found! Using
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/cpptraj
Preparing trajectories for simulation...
834 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
calculating complex contribution...
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
File "/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/MMPBSA.py",
line 104, in <module>
app.run_mmpbsa()
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError:
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy failed
with B.prmtop!
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Received on Sat Mar 12 2016 - 11:30:03 PST
