Dear Jason,
Thanks for your reply again,
As you had suggested I ran only GB and decomposition this time and it
works. But I have a question on this as well. When I checked
the "FINAL_DECOMP_MMPBSA.dat" file the output is displayed as follows:
(first few lines)
| Run on Sat Apr 9 02:57:26 2016
| GB non-polar solvation energies calculated with gbsa=2
idecomp = 2: Per-residue decomp adding 1-4 interactions to EEL and VDW.
Energy Decomposition Analysis (All units kcal/mol): Generalized Born solvent
Complex:
Total Energy Decomposition:
Residue,Internal,,,van der Waals,,,Electrostatic,,,Polar
Solvation,,,Non-Polar Solv.,,,TOTAL,,
,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of
Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of
Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean
MET
1,18.295510978,3.00342744569,0.134183242463,-2.97134730539,1.5582007752,0.0696152766149,-1.4887005988,5.53533189933,0.247300391234,-88.5866726547,5.18712206277,0.231743523032,1.18585871138,0.184138688854,0.00822670991063,-73.5653508695,3.6429465488,0.162754848878
*Could you please clarify a little bit on when to use idecomp=1 and when to
use idecomp=2. I looked at the manual and I am still not sure I understand
the difference between the two for my protein-protein complex.*
*Also,*
*I was expecting the outpput in nice column form so that I could directly
export everything in excel and analyse. But looks like here everything is
in paragraph form and I have no idea how to export these in excel or
similar program where I could analyze and plot these data. Could you please
suggest me something on this as well?? sorry for this trivial question.*
*REAL Problem:*
Now it works fine if I have gb and idecomp and it also works fine if I
have GB and PB but NOT decomposition in the script (as I mentioned before).
But as soon as I have all three i.e gb, pb and idecomp it fails with error
message saying that there is error in complex.prmtop.
*I looked at the _MMPBSA_complex_pb.mdout.0 and I don't even see any error
message. Is there any specific place you look for any error messages inside
this file?? I have copied and pasted some beginning and the ending results
from this file but I don't see any obvious error or something in here.*
*If you could help me identify the problem here I would be really grateful.*
*Thank you for your time!!*
File Assignments:
| MDIN: _MMPBSA_pb_decomp_com.mdin
| MDOUT: _MMPBSA_complex_pb.mdout.0
|INPCRD: _MMPBSA_dummycomplex.inpcrd
| PARM: cspz_fh7.prmtop
|RESTRT: _MMPBSA_restrt.0
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd.0
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, ipb=2, ntb=0, cut=999.0,
imin=5, idecomp=2, inp=1, igb=10,
END:
BDC 266 8.473 -0.374 -1.876 -1.746 0.000
BDC 267 12.421 -1.705 -10.623 11.065 0.000
BDC 268 10.116 -2.504 2.793 -10.984 0.000
BDC 269 10.687 -2.028 -15.311 1.104 0.000
BDC 270 8.389 -1.399 -4.163 0.381 0.000
BDC 271 8.536 -1.911 -3.524 -8.451 0.000
BDC 272 7.995 -0.581 -4.147 -5.448 0.000
BDC 273 4.249 -1.043 -50.372 -21.963 0.000
minimization completed, ENE= -.61339317E+04 RMS= 0.184696E+02
minimizing coord set # 225
On Fri, Apr 8, 2016 at 9:39 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
>
> > 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
>
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Received on Sat Apr 09 2016 - 17:00:03 PDT
