Hi,
I am trying to simulate a double - stacked beta sheet that involves thousands of atoms. It has repeating units in it, except for minor modifications at the boundaries. Instead of calculating the thousands of atoms of something repeating, I wanted to idealize the system, i.e make it infinite in size, so that I could use a unit cell or supercell with much fewer atoms.
I tried to do this using the PME method to simulate a quasi-one dimensional strand for a start, in a vacuum. Unfortunately, the PME method requires a box to enclose the structure with a buffer zone between the structure and the box. When I tried to make the buffer equal to zero in the direction of the length of the strand, AMBER doesn't like it.
So I gave up that approach, then read about the crystal simulation of AMBER with unitcell and other programs. But these programs such as unitcell seem designed for crystallographic pdb files from x-ray experiments with quite a bit of symmetry information. (The structure I am trying to simulate was studied with solid state NMR, and the PDB file I have doesn't have the same input format and not the kind of symmetry information as the x-ray pdb to my knowledge). So I was intimidated in pursuing along this direction further.
Furthermore, I have the intention of using QM/MM calculation involving the unit cell with much fewer atoms. The QM of QM/MM, I am told, handles around two hundred atoms or so.
If you have any suggestions how to simulate with unit cells or supercells, I would appreciate.
Cheers,
M
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, September 10, 2016 12:19:07 PM
To: AMBER Mailing List
Subject: Re: [AMBER] PME calculation for Vacuum?
On Fri, Sep 09, 2016, Mochena, Mogus D. wrote:
>
> I want to repeat a quasi-one dimensional strand surrounded by vacuum. My
> supercell has the following atoms:
>
> CRYST1 140.400 62.800 220.800 90.00 90.00 90.00 P 1 1
> ATOM 1 N ARG R 1 2.333 0.596 -18.467 0.00 0.00 RA11
> ATOM 2 CA ARG R 1 3.022 0.747 -17.157 0.00 0.00 RA11
> ATOM 3 CB ARG R 1 2.451 2.025 -16.474 0.00 0.00 RA11
> ATOM 4 CG ARG R 1 3.024 2.388 -15.085 0.00 0.00 RA11
> ATOM 5 CD ARG R 1 2.386 3.670 -14.524 0.00 0.00 RA11
> ATOM 6 NE ARG R 1 2.777 3.817 -13.084 0.00 0.00 RA11
> ATOM 7 CZ ARG R 1 2.100 4.604 -12.240 0.00 0.00 RA11
> ATOM 8 NH1 ARG R 1 1.261 5.548 -12.651 0.00 0.00 RA11
> ATOM 9 NH2 ARG R 1 2.235 4.447 -10.927 0.00 0.00 RA11
> ATOM 10 C ARG R 1 2.837 -0.485 -16.280 0.00 0.00 RA11
> ATOM 11 O ARG R 1 1.723 -0.970 -16.134 0.00 0.00 RA11
> ATOM 12 N ALA R 2 3.919 -1.039 -15.688 0.00 0.00 RA11
> ATOM 13 CA ALA R 2 3.827 -2.174 -14.783 0.00 0.00 RA11
> ATOM 14 CB ALA R 2 4.485 -3.430 -15.392 0.00 0.00 RA11
> ATOM 15 C ALA R 2 4.522 -1.786 -13.490 0.00 0.00 RA11
> ATOM 16 O ALA R 2 5.692 -1.397 -13.505 0.00 0.00 RA11
> ATOM 17 N ASP R 3 3.807 -1.836 -12.353 0.00 0.00 RA11
> ATOM 18 CA ASP R 3 4.045 -0.916 -11.257 0.00 0.00 RA11
> ATOM 19 CB ASP R 3 3.112 0.309 -11.491 0.00 0.00 RA11
> ATOM 20 CG ASP R 3 3.672 1.601 -10.957 0.00 0.00 RA11
> ATOM 21 OD1 ASP R 3 3.183 2.130 -9.923 0.00 0.00 RA11
> ATOM 22 OD2 ASP R 3 4.549 2.197 -11.639 0.00 0.00 RA11
> ATOM 23 C ASP R 3 3.765 -1.569 -9.901 0.00 0.00 RA11
> ATOM 24 O ASP R 3 2.852 -1.184 -9.173 0.00 0.00 RA11
> ATOM 25 N ALA R 4 4.545 -2.599 -9.519 0.00 0.00 RA11
> ATOM 26 CA ALA R 4 4.361 -3.271 -8.245 0.00 0.00 RA11
> ATOM 27 CB ALA R 4 5.072 -4.639 -8.221 0.00 0.00 RA11
> ATOM 28 C ALA R 4 4.827 -2.436 -7.058 0.00 0.00 RA11
> ATOM 29 O ALA R 4 5.961 -1.958 -7.016 0.00 0.00 RA11
What you want for this is the following command
set UNIT box {140.400 62.800 220.800}
Where "UNIT' is the name of the tripeptide unit. Use this command in place
of the "setBox" commands discussed in earlier emails.
Be aware that this is a very odd calculation, but I'm guessing you have a good
reason for wanting to proceed in this way, rather than just have a tripeptide
in a (non-periodic) vacuum.
....dac
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Received on Thu Sep 15 2016 - 14:30:03 PDT
