MmPbSaStat.py error

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Sajad Ahrari

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Aug 15, 2017, 7:37:15 AM8/15/17
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Dear Users,

I am trying to run "MmPbSaStat.py" after running the "g_mmpbsa -s ../../5es1_100ns_nowater.tpr -f  5es1_5RC_last5ns_dt80.xtc  -i pbsa.mdp -n ../../../MD_preparation/index.ndx -pdie 2 -pbsa -decomp" command. However, I was faced with the following error. Could you please help me know what I am missing? my input files are attached.

Thank you


D:\MD-Lab\Ahrari\MARK4\MARK4\analysis\inactive_drug_interaction\docking_AutoDock \5es1\1\MD-out\analysis\MMPBSA>python MmPbSaStat.py -m energy_MM.xvg -p polar.xv g -a apolar.xvg
Traceback (most recent call last):
  File "MmPbSaStat.py", line 303, in <module>
    main()
  File "MmPbSaStat.py", line 62, in main
    cTmp.CalcEnergy(args,frame_wise,0)
  File "MmPbSaStat.py", line 81, in CalcEnergy
    polEn = ReadData(self.PolFile,n=4)
  File "MmPbSaStat.py", line 245, in ReadData
    x_temp.append(float(data[i][j]))
IndexError: index 2 is out of bounds for axis 0 with size 2
MmPbSaStat.py
energy_MM.xvg
polar.xvg
apolar.xvg

g_mmpbsa Mailing List

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Aug 17, 2017, 9:01:26 AM8/17/17
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polar solvation energy is incomplete at last frame. If you open polar.xvg in any text editor, you can see that polar energy is not calculated for ligand and complex at time 95000 ps. Also, for apolar, no calculation is performed for last frame (95000 ps). Number of frames should be same in all three input files.

Khaled Darwish

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Dec 18, 2020, 6:54:11 PM12/18/20
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I am now trying to calculate the average and get the summary of free binding energy but this message appears

python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg

Traceback (most recent call last):
  File "MmPbSaStat.py", line 44, in <module>
    import numpy as np
ImportError: No module named numpy

Can you help me with this?
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