[gmx-users] center of box protein

[Justin A. Lemkul]

nahren manuel wrote:
> Dear GMX users,
> 
> I am trying to center my protein at the center of box using editconf. 
> When I view the same using ngmx, the protein seems to lie outside the box
> 
> neweditconf -f alapdb.pdb -bt cubic  -o boxpdb.pdb -c -center -0.156 
> -0.061 0.084 -d 1.5
> 

The protein appears "outside" of the box (which is irrelevant in a periodic 
system, anyway) because you're putting it there.  You've specified negative 
coordinates.  Gromacs builds all boxes from the coordinate origin into the 
quadrant where (x,y,z) are all positive.

> this one works, but the molecule is shifted.
> neweditconf -f alapdb.pdb -bt cubic -d 1.5 -o try.pdb
> 
> I want my molecule (geometrical )  center to be the center of the box 
> with -d 1.5.
> 
> 

Just use editconf -c -d 1.5; I don't know what "shifted" means above, because 
the combination of -c and -d should center the protein in the box (in fact, the 
use of -d automatically triggers -c).  Using -center overrides it with whatever 
you specify and is only necessary for custom placement.

-Justin

> Best,
> nahren
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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