Re: [AMBER] Defining the box dimensions while making the top and crd files

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 25 Jun 2015 09:39:03 -0400

On Wed, Jun 24, 2015 at 8:02 PM, Iqbal, Muhammad Sajid <iqbal.uleth.ca>
wrote:

> Hi Amber folks,
>
> Usually the box is defined using the combined vector values. How I can use
> the minimum and maximum coordinates to define the box? i have the
> coordinates as follows,
>
> maximum = {150.0 150.2343 150.22}
> minimum={-150.6945 -150.0 -150.34442}
> combined= {300.6945 300.2343 300.56442}
>
>
> mypdb = loadpdb mypdb.pdb
> set mypdb box {-150.6945 -150.0 -150.34442} {150.0 150.2343 150.22}
>

‚ÄčThe box is defined as 3 lengths and 3 angles. So the syntax *should* be
something like this:

mypdb = loadpdb mypdb.pdb
set mypdb box {300.6945 300.2343 300.56442 90 90 90}

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 25 2015 - 07:00:02 PDT
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