You need to be in the correct reference frame i.e. box center or the
origin (0, 0, 0)...
So, if image origin, center origin
center :1-462 origin
image origin center familiar
-tec3
On May 11, 2010, at 5:53 PM, "Sun, Yufang" <sunyu.iupui.edu> wrote:
> Dear Amber Users:
>
>
>
> We have problems with ptraj image.
>
>
>
> The protein moved out of the box after the actions of "center" and
> "image". This is the script I used:
>
>
>
> trajin prod.mdcrd
>
> center :1-462
>
> image origin center familiar
>
> trajout prod_imaged.mdcrd
>
>
>
>
>
> If I use the following script in which I deleted the command line
> "center :1-462", the imaged protein remains within the box.
>
>
>
> trajin prod.mdcrd
>
> image origin center familiar
>
> trajout prod_imaged.mdcrd
>
>
> However, when I search online or read AMBER manual or tutorial, they
> all suggested I need to center my solute first and then image. Could
> anybody please tell me whether we should center solute first or not.
> And if we do not center the solute first, is the imaged file
> reliable as we want to calculate some water molecules around certain
> residues.
>
>
>
> Thank you so much.
>
> Yufang
>
>
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Received on Wed May 12 2010 - 10:00:06 PDT
