On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.
The last line of the .gro file are the box vectors, not the center of the
system, so you are not, in fact, centering the protein. You are placing it in
the corner of the box yourself. The -center option overrides the -c option. If
you want the protein centered, omit -center in your editconf command.
-Justin
Thank you
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
Or not?
Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite
system
is an arbitrary location; you have to re-wrap the unit cell to achieve the
expected outcome. It's centered, it just may not look like it in the
current
representation.
-Justin
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I did a minimization of my structure. But the output seems a bit
strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#############
# PPPP #
# MPPPPM#
# PPPP #
# #
# #
#############
But the output of the minimization looks like this
#############
# PPPP#
#M MPPPP #
# PPPP #
# #
# #
##############
How can that be?
It's a triclinic representation of the unit cell. Nothing is wrong.
My box was created with:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
Is a dodecahedral box appropriate for a protein in a membrane? The
inherent
symmetry of a slab of any sort dictates that you should be using a
cubic
or
rectangular box. Dodecahedral and octahedral boxes are better for
systems
with
spherical symmetry, like globular proteins in water.
I put solvent in it with:
genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2>>logErr 1>>logOut
The mdp file for the minimization looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 1500
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
Can you please tell me how I can prevent my box to shift?
There is no box shift; it's just a visual representation of the
dodecahedral
box. You can "correct" it (for visualization purposes) by running
trjconv
-pbc
mol -ur compact.
-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
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========================================
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
========================================
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--
========================================
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
========================================
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