Just to add another option, packmol (
http://m3g.iqm.unicamp.br/packmol/home.shtml).
With a little bit of tinkering you can create almost everything. As far as I can see, there is a version of packmol bundled in with AmberTools.
// Gustaf
> On 10 Jun 2020, at 21:43, Raik Grünberg <raik.gruenberg.gmail.com> wrote:
>
> 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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>> http://www.raiks.de/contact.html
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>
>
> --
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> Raik Grünberg
> http://www.raiks.de/contact.html
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Received on Wed Jun 10 2020 - 23:00:05 PDT
