[gmx-users] calculate the size of protein

[hamid mosaddeghi]

Hi

if you found optimum size for your protein , you must use VMD ---> Tk console , I done it

for commands, please see manual of VMD or mailing list.



Best Regards

Hamid Mosaddeghi


________________________________
 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 February 2013, 13:19
Subject: Re: [gmx-users] calculate the size of protein
 
Hi KT,

If you set a box in any way, editconf writes the size of the box in
the input file, the dimensions of the system and the size of the
resulting box.

Cheers,

Tsjerk

On Sat, Feb 16, 2013 at 10:42 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com> wrote:
> Hi,
>
> What is the specific editconf command should i use to calculate the
> dimensions of fitting box of the protein ?
>
> Thanks and regards,
> KT
>
>
> On Fri, Feb 8, 2013 at 2:03 PM, Kieu Thu Nguyen <kieuthu2212 at gmail.com>wrote:
>
>> Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of
>> the protein
>>
>>
>> On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
>>
>>> Hi KT,
>>>
>>> What do you mean with size?
>>>
>>> - circumscribed radius: editconf
>>> - radius of gyration: g_gyrate
>>> - dimensions of fitting box: editconf
>>> - volume: g_sas
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com
>>> >wrote:
>>>
>>> > Dear all,
>>> >
>>> > I want to calculate the size of the protein. Which tool should i use for
>>> > this purpose ?
>>> >
>>> > Thanks and regards,
>>> > KT
>>> > --
>>> > gmx-users mailing list    gmx-users at gromacs.org
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > * Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> > * Please don't post (un)subscribe requests to the list. Use the
>>> > www interface or send it to gmx-users-request at gromacs.org.
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> >
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Biocomputing Group
>>> Department of Biological Sciences
>>> 2500 University Drive NW
>>> Calgary, AB T2N 1N4
>>> Canada
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists