Date: Fri, 16 Dec 2022 10:56:57 +0530
Respected Sir/Madam,
We had performed an MD simulation using PDB:4nct for studying its dynamics
and free energy profile. However the enthalpy calculated using the mmpbsa
method showed an unusual value of -833 kcal/mol with van der Waals value
showing an unusual -859.7860 kcal/mol with an exceptionally uncommon
standard deviation of 209.3551. Besides this the internal energy, mainly
its dihedral contribution is also not zero.
For verification we performed per-residue decomposition and found that two
cysteine residues (CYS 286 and CYS 312) involved in disulfide bond
formation are showing exceptionally high values of -396.77 & -396.57
kcal/mol respectively.
So please tell me what could be the possible reason for such an unusual
value and what may be the probable solution. I have also attached a
screenshot of the calculated value below for your reference.
Thanks and Regards
Kapil D. Ursal
PhD Scholar
BSBE Department
IIT Indore
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(image/png attachment: binding_enthaly.png)
