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
--
========================================
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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