Highly negative polar solvation energy

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Nidhi

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Jul 15, 2020, 7:18:17 AM7/15/20
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Dear Users,


I have calculated the binding free energy between a nanotube surface and protein by g_mmpbsa method. The polar solvation energy is coming out to be negative and approximately -1168 kJ/mol, due to this the total binding energy is highly negative approximately -2183.345 kJ/mol.

According to me this much of energy is not acceptable ideally I think?

 My simulation length is also very long approximately half micro second. I run two more independent simulation of the same system. But in one simulation polar solvation energy is positive and in other it is negative.

Please suggest me something. What could be the reason behind negative polar solvation energy and is this energy is acceptable?


I am sharing summary_energy.dat file of one simulation here,


#Complex Number:    1

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

   SUMMARY

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



 van der Waal energy      =       -1168.629   +/-    2.026 kJ/mol


 Electrostattic energy    =          -3.769   +/-    0.191 kJ/mol


 Polar solvation energy   =        -963.003   +/-   53.049 kJ/mol


 SASA energy              =         -45.949   +/-    0.198 kJ/mol


 SAV energy               =           0.000   +/-    0.000 kJ/mol


 WCA energy               =           0.000   +/-    0.000 kJ/mol


 Binding energy           =       -2183.759   +/-   54.315 kJ/mol


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

    END

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



Kindly suggest me something. I shall be very thankful to all of you.

Thank you in advance.

Hossein arzani

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Jul 26, 2020, 5:18:38 PM7/26/20
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Dear ....
Its an ideal results, its may be  result from conformation of protein such as positive amini acid or n. A.a interaction with nanotub. Pleas calculate residue decomposition and secondry structure analysis v.s main protein conformation

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