Hi Karl,
Thank you so much.
I have gone through according to your instruction. I need to build the
chain of 4-O-methylglucuronoxylan.
However, the problem is I am unable to add O (single molecule) with the
methyl ( derivative) . Otherwise, everything is okay.
Thank you again.
Kind regards,
Pinky
On Sun, Apr 5, 2020 at 3:18 AM Karl Kirschner <k.n.kirschner.gmail.com>
wrote:
> 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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> >
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>
--
Pinky
AL,US
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Received on Sun Apr 05 2020 - 16:00:02 PDT
