Hello Pinky,
You can find all of this information in the Amber18 manual, which can be
found at
https://ambermd.org/Manuals.php. Section 3.3 covers the
carbohydrate force field, including the residue naming convention (e.g.
Tables 3.5 - 3.8). Chapter 13 will teach you how to run the LEaP program
for constructing a 3D model (i.e. the topology and coordinate files need
for MD simulations) of given system of interest.
If you are still unsure how to proceed, then work on some tutorial (
https://ambermd.org/tutorials). You can also find additional information at
http://glycam.org/docs/forcefield.
Best regards,
Karl
On Sun, Apr 5, 2020 at 4:26 AM Pinky Mazumder <pmazumder67.gmail.com> wrote:
> Hi Amber Users,
>
>
> I want to build a chain of hemicellulose (amorphus).
>
>
> So, what will be the sequence command of 4-O glucuronuxylans (
> hemicellulose )?
>
>
> Could you please answer my question?
>
> Thank you.
>
> --
> Pinky
> UA
> AL,US
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Received on Sun Apr 05 2020 - 01:30:01 PDT
