I am using amber 9.
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Tuesday, May 11, 2010 7:59 PM
To: AMBER Mailing List
Subject: Re: [AMBER] protein moves out of the box when using ptraj center image
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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 12 2010 - 09:00:02 PDT
