Dear all,
I was just trying to calculate the per residue energy decomposition
following the tutorial given in Advanced Amber tutorial section. I already
ran PB and GB without any problem with the following script.
&general
startframe=500, endframe=3500, interval=5,
verbose=2, keep_files=2, strip_mask=':WAT,CL',
/
&gb
igb=5, saltcon=0.150,
/
&pb
inp=1, radiopt=0, istrng=0.15, fillratio=4.0
/
*But when I added the decomposition section (as follows) on the above
script (everything else is same) and tried to rerun I got the error message
during the complex PB calculation.*
*Could anyone guide me through this please? I have no idea why I am getting
that error message.*
&general
startframe=500, endframe=3500, interval=5,
verbose=2, keep_files=2, strip_mask=':WAT,CL',
/
&gb
igb=5, saltcon=0.150,
/
&pb
inp=1, radiopt=0, istrng=0.15, fillratio=4.0
/
&decomp
idecomp=2,dec_verbose=3,
/
Error Message:
Loading and checking parameter files for compatibility...
sander found! Using
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/sander
cpptraj found! Using
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/cpptraj
Preparing trajectories for simulation...
501 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/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/sander
calculating complex contribution...
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/sander
failed with prmtop complex.prmtop!
Thank you for your time!!
RT
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Received on Fri Apr 08 2016 - 12:30:04 PDT
