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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Received on Thu Oct 29 2020 - 03:30:02 PDT
