Hi Matthew,
I dont think Amber supports covalent bonds across the PBC box edges.
Couldnt you simulate a supercell, say 2x2x2 crystal unit cells, that allows
your complete protein to fit into one simulation box?
Kind Regards,
Thomas
On Fri, Jul 14, 2023 at 5:33 AM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear Amber community,
>
> How can I simulate a crystal lattice of a protein where the protein does
> not fit within the unit cell? That is, there would need to be covalent
> bonds across the simulation box boundary, which doesn’t make sense to me.
> I’d appreciate any advice/suggestions to deal with this situation?
>
> Best,
> Matthew
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 14 2023 - 02:00:02 PDT
