[gmx-users] Coarse Grain using martinize.py

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 26 22:59:51 CET 2016

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,

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 khourshaei shargh (khourshaeishargh at mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran
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