[gmx-users] problem with the translate option of editconf

[Erik Marklund]

Ozge Engin skrev:
> Hi all,
>
> I am trying to translate the peptide within the simulation box. I have 
> a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the 
> peptide on top of the box. In order to that I used the following 
> command line:
>
> editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb
>
> The peptide is not translated, but sitting at the center of the box. 
> Why is the case? Any suggestions?
>
> Thanks in advance
>
> -- 
> Ozge Engin
>
Because -c is implied by -box. excerpt form editconf -h output:

-[no]c       bool   no      Center molecule in box (implied by -box and -d)

You'll have to do the -box and the -translate in two sequential passes 
through editconf.

-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys