This just means that you have not run long enough MD trajectories,
i.e. your free energy calculations have not converged ... if you do,
the difference between different trajectories should be within the
uncertainties of reported free energies.
Ray
On Mon, Jun 11, 2012 at 2:08 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>
> Hello All
> I have four protein-DNA complexes first is wt, second DNA mutant, third protein
> mutant and fourth both mutant. I have to calculate binding free energy of these
> complexes.
>
> When I ran MD simulation of all these and calculate binding free energy, I got
> binding free energy as follows:
> First MD
>
> wt = -77.4 kcal/mol
> DNA mutant = -59.7 kcal/mol
> protein mutant = -77.2 kcal/mol
> both mutant = -73.9 kcal/mol
>
>
> Second MD run
>
> wt = -72.9 kcal/mol
> DNA mutant = -91 kcal/mol
> protein mutant = -74 kcal/mol
> both mutant = -86.8 kcal/mol
>
> Is it possible to reproduce the result? I also claulated residue wise energy
> decomposition there also I am getting diffrent result residue which is not
> involve in interaction energy of that residue in first MD run is unfavorable
> (2.9 kcal/mol) but in second MD run become favorable (-10.7 kcal/mol). So I am
> not able to justify my result.
>
> Is here my approach to claulate bindng free energy is correct, i.e. run two MD
> simulation and then calculation of binding free energy is correct so that I can
> also calculate STD of two result or run MMPBSA two times of a single MD run and
> calculate STD of two MMPBSA calculation ?
>
> Can anybody please suggest me
>
>
>
> With regards
>
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
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Received on Mon Jun 11 2012 - 09:00:03 PDT
