no- not amber10. use ambertools from the amber web site.
On 5/12/10, Sun, Yufang <sunyu.iupui.edu> wrote:
> 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
>> ===================================================================
>>
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>> 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
>
--
===================================================================
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
===================================================================
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Received on Wed May 12 2010 - 10:00:09 PDT
