Re: Regarding minimization of a protein

From: Deepshikha Ghosh 19310001 (
Date: Mon Mar 28 2022 - 05:24:51 CDT

Thankyou so much for your response. I had a follow up question on this,
that these constraints should then be removed while doing equilibration in
the next step?


On Mon, Mar 28, 2022 at 3:00 PM Anup Prasad <> wrote:

> 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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