Hi,
The box is usually created by the command
solvatebox
which solvates your system and prepare the box information.
If you have your system solvated using other software,
and you know the box size, you can use the command:
set xxx box {angl, box_x, box_y, box_z}
while angl is the box angle, for cubic box it is 90.0, and
box_x, box_y and box_z is the size of you box.
Sincerely,
Wei
On Apr 6, 2009, at 7:49 AM, Tomasio, Susana wrote:
>
> Thank you for your reply.
>
> I am trying to do that example with jac.pdb, but I don't know how to
> create the box in sleap.
>
> Do I have to do everything in sleap?
>
> Thanks a lot,
>
> Susana
>
> -----Original Message-----
> From: amber-bounces.ambermd.org on behalf of David A. Case
> Sent: Mon 4/6/2009 1:47 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber with AMOEBA force-field
>
> On Mon, Apr 06, 2009, Tomasio, Susana wrote:
>>
>> I am trying to use amber with the amoeba force-field.
>> Does anyone have an example/tutorial of see how it works.
>
> Look at the examples/tests in amber10/test/sleap/amoeba. Those should
> work, and give you sample inputs and outputs.
>
> ...dac
>
>
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Received on Wed Apr 08 2009 - 01:08:49 PDT
