From: Deepshikha Ghosh 19310001 (deepshikha.ghosh_at_iitgn.ac.in)
Date: Mon Mar 28 2022 - 05:32:58 CDT
Thankyou for your response, I understood the concept behind this.
On Mon, Mar 28, 2022 at 3:54 PM Deepshikha Ghosh 19310001 <
deepshikha.ghosh_at_iitgn.ac.in> wrote:
> 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?
>
> Regards
>
> On Mon, Mar 28, 2022 at 3:00 PM Anup Prasad <anup.prasad_at_monash.edu>
> 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 <
>> deepshikha.ghosh_at_iitgn.ac.in> 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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