are you using the most recent ambertools?
On 5/11/10, 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 11 2010 - 17:30:03 PDT
