Re: [AMBER] protein on gold surface

From: Casalini Tommaso <>
Date: Mon, 8 Jun 2020 10:14:47 +0000

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:

It is not exactly your system but you may find some useful insights.

Hope this helps!


Da: Raik Grünberg <>
Inviato: giovedě 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 Grünberg
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Received on Mon Jun 08 2020 - 03:30:02 PDT
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