Hi Carlos:
OK, I will try again using amber 10, and let you know whether it works.
Yufang
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Wednesday, May 12, 2010 11:45 AM
To: AMBER Mailing List
Subject: Re: [AMBER] protein moves out of the box when using ptraj center image
that is many versions old- please download and use the newest ambertools.
On 5/12/10, Sun, Yufang <sunyu.iupui.edu> wrote:
> 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
>
--
===================================================================
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 - 10:00:04 PDT
