On Fri, Dec 16, 2022, Kapil Ursal via AMBER wrote:
>
>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.
We don't have enough information here. There could be one bad frame in the
calculation, or the structures might have large outliers, etc. Look at the
distribution of enthalpy values, and the structures around the two cysteines
you cite. Basically, detective work at your end is needed here to dig down
beneath just the average values.
...good luck...dac
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Received on Wed Dec 21 2022 - 06:30:03 PST
