Thanks a lot Tommaso! That sounds like exactly what we were looking for.
On Mon, Jun 8, 2020 at 1:15 PM Casalini Tommaso <
tommaso.casalini.chem.ethz.ch> wrote:
> Dear Raik,
>
> a nice way to build your system is using the AddToBox utility implemented
> in AmberTools.
>
> I have employed it to solvate a lipid bilayer (that lies in the xy plane)
> only along z direction - the system is different, but the fundamental aim
> is the same.
>
> Since you need to provide a pdb as input, you must set box dimension
> properly: box size along x and y will be the size of your surface, while
> you can set a suitable value of the box size along z.
>
>
> In general, I would like to suggest to have a look at this paper:
>
>
> https://pubs.rsc.org/en/content/articlehtml/2013/nr/c3nr01799k
>
>
> It is not exactly your system but you may find some useful insights.
>
>
> Hope this helps!
>
> Tommaso
>
> ________________________________
> Da: Raik Grünberg <raik.gruenberg.gmail.com>
> Inviato: giovedì 4 giugno 2020 20:26:15
> A: AMBER Mailing List
> Oggetto: [AMBER] protein on gold surface
>
> Dear Amberians,
>
> we are constructing biosensors in the lab where we couple a protein to a
> layer of 1,6-hexanedithiol which is in turn covalently attached to a gold
> surface. We would now like to simulate the whole thing in Amber. We roughly
> followed tutorial 27 to get a gold / water parmtop. However, this
> particular tutorial simulates the metal / peptide system in gas phase. Are
> there any more advanced examples to be found somewhere?
>
> So here comes my first very basic question: My naive assumption was that I
> would build a periodic box with a couple of atoms-thick gold layer "at the
> bottom" reaching right to the x and y edges. Water would then be above and
> below but not around the metal -- kind of like a multi-storey car park with
> golden floors stretching to infinity -- well, or more like a membrane
> simulation. But does that even make sense? Can the PME properly model a
> continuous metal layer?
>
> A practical problem is that such a system cannot, as far as I see, be built
> with the tleap solvatebox command. As waters are always placed all around
> in all dimensions (although I haven't tried thickness=0 yet). My tentative
> workaround would be to try first building a system with a flat gold
> rectangle surrounded by water and then trim this system back to the edge of
> the gold. Doesn't sound particularly elegant though and I am not sure how
> to perform the trimming. Are there any better suggestions?
>
> Thanks a lot in advance for any suggestions or hints.
> Best regards
> Raik
>
>
> --
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Received on Wed Jun 10 2020 - 13:00:03 PDT
