Error executing MmPbSaStat.py file

[Flavio Seixas]

I managed to run g_mmpbsa program and generate all output files without any problem (apolar.xvg, polar.xvg, contrib_MM.dat, etc ...)

But when I run the script MmPbSaStat.py, the following problem occurs:

[Flavios @ hercules 5-MMPBSA] $ python -m MmPbSaStat.py energy_MM.xvg -p polar.xvg -a apolar.xvg
   File "MmPbSaStat.py", line 142
     self.FinalAvgEnergy = AvgEn
                               ^
TabError: inconsistent use of tabs and spaces in indentation

I am using a protein-cofator-ligand system.
I made an index file using:

protein_FMN  LIGAND

could it be affecting the calculation at someway?

Best regards,

Flavio

[g_mmpbsa Mailing List]

Hi,

You are not running the script in correct way. "-m" option should be used with MM energy file and not with the python script.

Thanks. 

[Flavio Seixas]

Hi,
Excuse-me for the insistence, but I do not understand how I am executing the script in the wrong way...
I am doing exactly as the tutorial says:

Average Binding Energy Calculation

To calculate average binding energy, a python script MmPbSaStat.py is provided in the g_mmpbsa package. For details about this script, please click on this link. To execute this script, above obtained files are required as the inputs.

To calculate average binding energy by direct method, execute following command:

python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg (or sasa.xvg)

Please, could you specify what I am doing wrong?

For calculations using Protein_LIG systems, this command was working fine...

Regards,

Flavio

[Thyageshwar Chandran]

Dear All, 

I am having some issue with the output . The problem is there is high error rate with the binding energy, can anyone please suggest any ways to decrease the same 

===============

  5    SUMMARY

  6 ===============

  7 

  8 

  9  van der Waal energy      =          -0.042   +/-    0.051 kJ/mol

 10 

 11  Electrostattic energy    =          -4.044   +/-    1.915 kJ/mol

 12 

 13  Polar solvation energy   =          48.694   +/-  500.363 kJ/mol

 14 

 15  SASA energy              =          -0.079   +/-    1.561 kJ/mol

 16 

 17  SAV energy               =           0.000   +/-    0.000 kJ/mol

 18 

 19  WCA energy               =           0.000   +/-    0.000 kJ/mol

 20 

 21  Binding energy           =          44.528   +/-  500.321 kJ/mol

 22 

 23 ===============

 24     END

 25 ===============

thanks in advance 

thyagesh

 

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[g_mmpbsa Mailing List]

[Flavios @ hercules 5-MMPBSA] $ python -m MmPbSaStat.py energy_MM.xvg -p polar.xvg -a apolar.xvg

As you can see above, you have given the "-m" flag between python and MmPbSaStat.py. However, "-m" is for MM energy file and it should be after MmPbSaStat.py.

[Flavio Seixas]

Thank you for your attention.

However, I did not make myself clear. Sorry for that.

No matter the position of the "-m" flag I always observe the same error:

[flavios@hercules 5-MMPBSA]$ ls -l
total 95012
-rw-rw-r--. 1 flavios flavios   529665 Sep 26 13:15 apolar.xvg
-rw-rw-r--. 1 flavios flavios 20014656 Sep 26 13:15 contrib_apol.dat
-rw-rw-r--. 1 flavios flavios 20014656 Sep 26 13:13 contrib_MM.dat
-rw-rw-r--. 1 flavios flavios 20014656 Sep 26 13:15 contrib_pol.dat
-rw-rw-r--. 1 flavios flavios   424544 Sep 26 13:13 energy_MM.xvg
-rw-rw-r--. 1 flavios flavios 36005709 Sep 20 17:32 index.ndx
-rw-------. 1 flavios flavios     7820 Jun 11  2014 MmPbSaDecomp.py
-rw-------. 1 flavios flavios    12287 Sep 17  2013 MmPbSaStat.py
-rwxrwxrwx. 1 flavios flavios     2918 Jun 11  2014 pbsa.mdp
-rw-rw-r--. 1 flavios flavios   221322 Sep 26 13:15 polar.xvg

[flavios@hercules 5-MMPBSA]$ python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg

  File "MmPbSaStat.py", line 142
    self.FinalAvgEnergy = AvgEn
                              ^
TabError: inconsistent use of tabs and spaces in indentation

[flavios@hercules 5-MMPBSA]$

Regards,

Flavio

[g_mmpbsa Mailing List]

It means script is modified. It is a simple syntax error due to indentation problem. I would suggest to download the script from GitHub (https://github.com/RashmiKumari/g_mmpbsa/blob/master/tools/MmPbSaStat.py) .