For the steps to go through to have an embedded protein in
membrane bilayer Justin has made a nice tutorial ... look in
the mail list archive
On Dec 15, 2009, at 6:21 PM, sunny mishra wrote:
ok. Thats the step where I am really confused that how to apply the
PR on my system file (system file is a combination of CG protein and
CG lipid).
On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
Well if you put a protein CG into your DPPC bilayer you'll have to
be soft on the start. PR is one way to do it and you can do similar
to when doing on a atomistic simulation.
On Dec 15, 2009, at 6:13 PM, sunny mishra wrote:
Alright thanks. So should I do it for proteins?
On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
No need of position restrained simulation with the CG lipids.
CG is very forgiving :))
For proteins it is more delicate.
On Dec 15, 2009, at 6:02 PM, sunny mishra wrote:
Thanks for the reply. I have another quick question that If I have
to do the Position Restrained EM Simulation of CG DPPC lipid then
is it done the same way we do for atomistic structure of proteins
like by defining the LIPPOSRES in the lipid.mdp file or while
using MARTINI forcefield is there any other way of doing the
Position Restrained EM simulation of CG DPPC lipids?
On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole
<x.peri...@rug.nl> wrote:
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's
Website and I am trying to convert the Atomistic structure to CG
structure. For that I am using atom2cg script provided by the
martini folks but it doesn't convert the Atomistic structure to CG
structure. atom2cg script works well for converting the atomistic
structure of PROTEIN to CG structure of protein but for LIPIDS it
doesn't work. Does anyone know how can I convert the 128 DPPC
atomistic structure of lipids to CG structure.
This is correct. atom2cg is only working for proteins ...
I would suggest you take dppc structure file from the martini web
site!
Best Regards,
Sunny
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