Francesco Pietra wrote:
Hi:
This is to ask how to proceed to minimize a CG ensemble made of a
transmembrane multimer with pore region immersed in a hydrated DPPC
bilayer and extracellular region immersed in water. Total height 18
nm, width 10 nm in the extracellular region and 6 nm in the pore
Are these the dimensions of your protein?
region. No clashes/contacts at 1 Angstrom vdw overlap. That is,
cavities had been created - in two steps - with 2.5 Angstrom margin
into both the bilayer surrounding the pore and the water surrounding
the extracellular region.
Everything worked fine up to creating the topol.tpr, perhaps using a
too small -box 15 15 15. Minimization by steepest descents (em.mdp
below)
That box is clearly too small to accommodate your system, given the dimensions
listed above.
cpp = /usr/bin/cpp
define = -DFLEX_SPC
You're using SPC water in a coarse grain model? This doesn't make sense to me -
an atomistic solvent with CG protein?
<snip>
The commands:
genbox -cp my.pdb -box 15 15 15 -o my.gro
Indeed, this would call spc216.gro as the default solvent (-cs), which I don't
understand.
and then the system topology with
grompp -f em.mdp -c my.gro -p my.top -o topol.tpr
and then
mdrun -v -s topol.tpr
==============
I found no way to build the system using gromacs scripts alone, i.e.,
combining preformed gromacs canonical boxes. The way I described above
works fine in Amber with all-atom ensemble.
==========
It's been many weeks now that you've posted some issues with your CG system, and
I'm sorry but I can't recall - have you run through my membrane protein
tutorial? It should be easily quite extended to a CG system. All of the
fundamentals are the same as far as positioning the system, etc. go:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I would appreciate very much an opinion about the feasibility of such
an approach with gromacs, or, hopefully, if a further solvation step
is needed before minimizing. I did not try with a larger box, or if
the protein+DPPC alone should be solvated with gromacs commands (I
avoided this way because I want to leave the DPPC not solvated from
the sides)...
Such systems can certainly be built with Gromacs. Unwanted solvation comes from
improper box definition. I believe I suggested this before - don't define the
box when using genbox, which uses a tiled algorithm to fill the unit cell. Do
all box manipulation and positioning with editconf. I have found it to be more
reliable.
-Justin
--
========================================
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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