Hi,
On Sun, Jan 6, 2019 at 6:02 AM Elvis Martis <elvis.martis.bcp.edu.in> wrote:
>
> Then remove the rotational and translation motions using autoimage.
Slight correction here - 'autoimage' will only perform imaging. In
order to remove global rotational/translational motion you will have
to fit your coordinates to a reference frame via a.g. the 'rms'
command. For the purposes of calculating RMSF it's usual to fit to an
averaged structure. There is an example given in the 'atomicfluct |
rmsf' section of the Amber18 manual (page 631).
-Dan
>
> Using the "atomicfluct" command you can compute the rmsf.
>
> Using "byres" keyword to compute rmsf residuewise.
>
>
> Best Regards
>
> Elvis A F Martis
>
> Molecular Simulations Group,
>
> Department of Pharmaceutical Chemistry,
>
> Bombay College of Pharmacy,
>
> Kalina, Santacruz [E],
>
> Mumbai 400098,
>
> INDIA.
>
> Institute Web-address: www.bcp.edu.in<http://www.bcp.edu.in>
>
> Research Group Web-address: www.profeccoutinho.net.in<http://www.profeccoutinho.net.in>
>
> Personal Web-address: www.elvismartis.in
>
>
>
> ________________________________
> From: Akshay Prabhakant <akshayresearch16.gmail.com>
> Sent: 06 January 2019 14:53
> To: AMBER Mailing List
> Subject: [AMBER] RMSF in amber
>
> I have multiple trajectory files for my protein system(multiple .nc files).
> How to find the rmsf(root mean square FLUCTUATION) using these .nc files?
> Thanks in advance.
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Received on Mon Jan 07 2019 - 08:00:03 PST
