My reading of what you need is
setbox unitname vdw 10.0 10.0 10.0
Bill
On 9/9/16 2:10 PM, Mochena, Mogus D. wrote:
> Dear Charles and Bill,
>
> Thank you very much for your prompt responses. I tried both
>
> setBox unitname vdw [0.0 10.0 10.0]
>
>
> tleap doesn't accept the command that I based on
>
> usage: setBox <unit> vdw|centers [ clearance | <clearance_xyz_list> ]
>
>
> It complains "improper number of arguments".
>
>
> 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
>
>
> Thanks for the help.
>
>
> ________________________________
> From: Charles Lin <clin92.ucsd.edu>
> Sent: Friday, September 9, 2016 2:51:12 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] PME calculation for Vacuum?
>
> You can use setBox command when you're running Leap to set the simulation box and not solvate the system with water.
>
> -Charlie
> ________________________________________
> From: Mochena, Mogus D. [mogus.mochena.famu.edu]
> Sent: Friday, September 09, 2016 11:36 AM
> To: amber.ambermd.org
> Subject: [AMBER] PME calculation for Vacuum?
>
> Hi All,
>
> My attempt to make a periodic calculation with ntb=1, resulted in the following error message:
>
> peek_ewald_inpcrd: Box info not found in inpcrd.
>
>
> The message complains about lack of periodic box. It seems to me such a box is created with solvatbox command which is for solutes surrounded by solvents.
>
>
> Earlier messages to similar problem suggest to turn off periodic calculation with ntb=0. Is there a way to do a periodic calculation in vacuum?
>
>
> Thanks,
>
> Mogus
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Received on Fri Sep 09 2016 - 14:30:03 PDT
