> On Apr 8, 2016, at 3:12 PM, Arati Paudyal <apsilwal123.gmail.com> wrote:
>
> 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!
What is the error message in _MMPBSA_complex_pb.mdout.0?
I would also suggest that, when doing decomposition analysis, stick to just using GB. It is much more straightforward to approximate a decomposed potential with GB.
HTH,
Jason
>
>
> Thank you for your time!!
>
> RT
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 08 2016 - 19:00:03 PDT
