Hi Thomas:
Thanks for your advise. Actually I tried the following scripts, but it does not work either:
center :1-462 origin mass
image origin center familiar
Yufang
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Thomas Cheatham [tec3.utah.edu]
Sent: Wednesday, May 12, 2010 12:40 PM
To: AMBER Mailing List
Cc: AMBER Mailing List
Subject: Re: [AMBER] protein moves out of the box when using ptraj center image
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 - 10:30:06 PDT
