[gmx-users] Coarse Grain using martinize.py

[Jagannath Mondal]

Dear Tsjerk
  I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an atomistic
simulation), how do I generate a coarse-grained martini counter-part of
that specific atomistic snapshot ?

Your suggestion will be very helpful.

On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ali,
>
> The current version of martinize is for coarse graining proteins and
> there's a version for nucleic acids. Lipids are not supported yet. These
> you could forward map with the program backward, but why the hassle as you
> can also directly build the coarse grain membrane/solvent system with
> insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane).
>
> Hope it helps,
>
> Tsjerk
> On Feb 26, 2016 22:36, <khourshaeishargh at mech.sharif.ir> wrote:
>
>
>
> Dear all
> I want to simulate a system of 128 DPPC with 3655 water molecule which its
> .pdb file is available on professor tielman website. I want to Coarse
> grain it but apparently at first i should turn the pdb file into
> appropriate type for using with martini. I understood, I should use marti
> ize.py to convert the pdb but I dont know how. Also the tutorial wasnt
> helpful. Could anyone give me the direct command to do this ?
> best regards
> Ali
> ==================
> Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
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