Sorry, the numbers should be in a list, so
setbox unitname vdw {10.0 10.0 10.0}
Bill
On 9/9/16 2:19 PM, Bill Ross wrote:
> 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 - 15:00:03 PDT
