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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 15 2018 - 12:00:03 PST
