[gmx-users] problems with editconf

[reisingere at rostlab.informatik.tu-muenchen.de]

Ah okey,
Thank you!

>
>
> On 7/3/12 5:10 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to put my protein in the box with editconf but when I look at it
>> it
>> is always at the border of the box and not at the center. I tried it
>> with
>> those two commands:
>>
>> editconf -f 3m71.gro -o 3m71_box.gro -center 4.59340   4.59470   5.17330
>> -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
>>
>> editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0
>> 2>>logErr
>> 1>>logOut
>>
>> With the first command it is at the upper border and with the second
>> command it is at the right border. The coordinates of the firs command
>> are
>> from the 3m71.gro file.
>>
>> Can you please tell me what is wrong?
>>
>
> Nothing.  When visualizing the unit cell, it will appear as a triclinic
> box with
> the protein in a seemingly random location.  You can re-wrap the unit cell
> with
> trjconv -pbc mol -ur compact (which requires a .tpr file) to see the
> dodecahedral unit cell with everything placed as you would expect.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * 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
>