You will need a very specific and detailed definition of the lignin
polymer you are trying to model. It will be best if you can find an
experimental 3D structure with coordinates for most or all of the
atoms. You can probably recover if the hydrogens are missing. If
there is not an experimental structure, you will need detailed
geometric information regarding bonding and linkage geometries.
Usually the latter also comes from experiment.
Do you have any such structural data?
On Wed, Jun 17, 2020 at 8:07 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Hi David,
>
> Thank you. According to your instructions, it works.
>
> Though I have built the monomer of lignin using graphic antechamber, I am
> unable to make the polymer of it.
>
>
> Would you please guide me in this regard?
>
> Thanks in advance.
>
> Regards,
> Pinky
>
> On Thu, Jun 11, 2020 at 9:13 AM David A Case <david.case.rutgers.edu> wrote:
>
> > On Wed, Jun 10, 2020, Pinky Mazumder wrote:
> > >
> > >I am trying to save the *parm7 and rst7 *file of cellulose-lignin
> > structure
> > >from xleap. It is saying that *'' the files have some atoms not in the
> > >residue templates''.*
> >
> > This means that atoms/residues in your input PDB files are not present
> > in the library files you loaded.
> >
> > >
> > >To solve this problem, what should I do?
> >
> > LEaP should give you information about which atoms are unmatched. Look
> > at the loaded libraries (using a text editor), and compare them to what
> > is in your input PDB file. Generally, you would then edit the PDB file
> > to make the atom and residue names match up.
> >
> > ...good luck....dac
> >
> >
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> >
>
>
> --
> Pinky, Sharmi
> AL,US
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Jun 19 2020 - 21:30:04 PDT
