Follow the tutorial once you get your .cif into a PDB:
./UnitCell -p <your structure> -o <output>
./PropPDB -p <output form UnitCell> -o <tiled structure> -ix <replicas in
x> -iy <...> -iz <...>
On Thu, Nov 15, 2018 at 4:16 PM Ali Khodayari <
ali.khodayari.student.kuleuven.be> wrote:
> Dear David,
>
> Thank you for your response. Indeed, your work will be appreciated.
>
> I can build the pdb for the cellulose crystal lattice, using its CIF file
> in Materials Studio. How can I then replicate this structure in three
> dimensions?
>
> Regards,
> Ali
>
> > On 15 Nov 2018, at 20:41, David Cerutti <dscerutti.gmail.com> wrote:
> >
> > If your structure is amenable to tesselation, then you can use the
> xtalutil
> > programs in AmberTools to do it. See this tutorial:
> >
> > http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
> >
> > But, the problem is that you'll need something that's ready to tesselate
> in
> > three dimensions. See if you can find anything in the PDB for this
> > problem. I'm working on extensions to cpptraj that will allow you to
> work
> > with all of the independent copies of your asymmetric unit as if they
> were
> > one ergodic unit.
> >
> > Dave
> >
> >
> > On Thu, Nov 15, 2018 at 2:29 PM Ali Khodayari <
> > ali.khodayari.student.kuleuven.be> wrote:
> >
> >> Dear Amber users,
> >>
> >>
> >>
> >> I am trying to build a crystalline cellulose structure in amber. I
> tried to
> >> use "sequence" to build a chain of glucose in tleap using GLYCAM_06j-1
> >> force
> >> field as follows:
> >>
> >>
> >>
> >> cellulose = sequence {ROH 4GB 4GB 4GB 4GB 0GB}
> >>
> >> set cellulose tail cellulose.6.O4
> >>
> >>
> >>
> >> The question is, how can I use this chain to produce a crystal having
> the
> >> lattice parameters of cellulose. In other words, is there a proper way
> to
> >> build a 6*6 structure, using the above-mentioned chain, satisfying the
> >> lattice parameters of crystalline cellulose?
> >>
> >>
> >>
> >> Thank you in advanced.
> >>
> >> Kind regards,
> >>
> >> Ali
> >>
> >> _______________________________________________
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> >>
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>
>
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Received on Thu Nov 15 2018 - 13:30:04 PST
