Re: Regarding minimization of a protein

From: Anup Prasad (
Date: Mon Mar 28 2022 - 04:30:39 CDT

If you fix the backbone atoms of protein during minimization, the secondary
structure does not change. However, in a few cases when the initial
configuration of the peptide appears helical or sheet-like structure (But
not secondary structure by DSSP) then a slightly secondary structure
appears in those peptide segments during minimization. You should check
whether you have used the backbone fixation or not for minimization.

On Mon, 28 Mar 2022 at 20:08, Deepshikha Ghosh 19310001 <> wrote:

> I am currently minimizing a protein using NAMD and it seems to show
> fluctuations in the secondary structure content after minimization. Can
> this happen?

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