Thank you very much. I will try your suggestion and try to understand it as well. I am new to AMBER.
________________________________
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 Sat Sep 10 2016 - 10:00:02 PDT
