Hi Dr. Horn,
Thanks for your reply.
But, using a carbohydrate builder, I can build a single chain. When it is
the case of cellulose bundles (cellulose crystals), that is difficult to
build it using AMBER. that is why I have used cellulose builder where I can
make easily (6*6) cellulose crystals.
But finally, when I am importing in AMBER, it is not recognized by xleap.
Any suggestions so that I can overcome this problem?
Thank you.
sIN
On Thu, Oct 29, 2020 at 5:24 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Hi,
>
> it seems that the atom names in your pdb file are incorrect.
>
> Maybe you want to have a look in the Amber20 manual ("3.3. Carbohydrates
> " and "13.7. Building oligosaccharides ..."). You may also want to visit
> http://www.glycam.org/ , the site is referenced in the manual, where a
> browser-based carbohydrate builder is available as tool, which probably
> yields pdb files much more consistent with the Amber/glycam naming scheme.
>
> Regards,
>
> Anselm
>
>
>
> On 10/29/2020 06:47 AM, Pinky Mazumder wrote:
> > Dear AMBER Users,
> >
> > There is a toolkit named cellulose builder
> > (https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.22959) which I
> have
> > used to generate the cellulose bundles. The output of this toolkit is
> > (.pdb) files and (.psf) file.
> >
> > When I am importing these (.pdb) files in xleap, it gives the message
> > attached herewith.
> >
> > *Leap added 72000 missing atoms according to residue templates:*
> > *37440 Heavy*
> > * 34560 H / lone pairs*
> > *The file contained 31680 atoms not in residue templates*
> >
> > Could you please give me any suggestions to solve this issue?
> >
> > Any help would be appreciated.
> >
> > Thank you!
> >
> >
> > Regards,
> >
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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--
Pinky, Sharmi
AL,US
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Received on Thu Oct 29 2020 - 10:00:03 PDT
