From: Andre Farias de Moura (moura_at_ufscar.br)
Date: Fri Feb 12 2021 - 04:59:00 CST
Dear Raman,
Although most people to date have relied on normal mode analysis to predict
IR features, MD simulations can be used as well, with the advantage of
sampling multiple energy minima (as compared to the single minimum in
energy minimization protocols). It does not matter whether you have a large
protein or small molecule in vacuum, procedures will be pretty much the
same (maybe you might want to look at the TRAVIS program, which can handle
MD simulations to extract IR).
Please mind that you will still need normal mode analysis to assign the IR
bands, since MD-based spectra yield only the convoluted bands.
Regards
Andre
On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh <
ramanpreetsingh_at_hotmail.com> wrote:
> Dear All,
>
> I posted this earlier but received no directions. Reposting the same in
> case someone who might help me missed it.
>
> Thanks in advance.
>
> RPS
>
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> ------------------------------
> *From:* Raman Preet Singh
> *Sent:* Monday, January 18, 2021 11:51:23 PM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>
> *Subject:* Infrared spectrum prediction
>
> Dear All,
>
> I have come across some papers where MD has been used to predict IR
> spectrum of proteins. Is it possible to predict IR spectrum of small
> organic molecules from NAMD simulations? Can changes in IR spectra due to
> interactions between two molecules (H-bonding, pi-pi interactions, etc ) be
> also predicted? Any papers, tutorials, scripts, etc. would be highly
> appreciated.
>
> Thanks in advance.
>
> Regards,
> Raman
>
>
>
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