[gmx-users] Energy minimization result problem

[Mark Abraham]

Hi,

Proteins do not have a single holy structure, nor is any given quantity of
MD going to find it, if it exists. Neither is there a single metric of
suitability - backbone strain as measured by Ramachandran plot deviations
could easily be the result of accommodating worse problems while stuck in a
local minimum. You can get zero deviations by unfolding the whole protein,
but that isn't going to tell you anything. Or the deviations could be good
things, because parts of your structure are atypical, but healthy.

Mark
On Apr 13, 2014 9:52 AM, "neha_bharty" <nehabharty123 at gmail.com> wrote:

> Hello Justin Lemkul
>
> Thank you very much for your reply.
> I also preformed MD for 15 ns. After MD I check my protein model with
> Ramachandran Plot using Online Procheck server. But the result was same as
> after energy minimization. The residues which were present in allowed
> region
> was again less than that of previous protein.
> As I am new in gromacs I don't have much idea.
> In my view I guess after energy minimization and MD the residues which were
> present in allowed region of Ramachandran plot should be increases.
> And if it decreases it means the previous model is better.
> Is there any other way to check my protein model is better after energy
> minimization and MD or not??
>
> If require I can also send the .mdb file I have used for MD.
>
>
>
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