[gmx-users] using martinize.py to martinize two chains complex

Lingyun Wang lywang at uab.edu
Wed Sep 5 23:53:29 CEST 2012

Hi all,

There are two chains in the complex.pdb file, but martinize.py only recognize them as one chain. What can I do to generate two chains in the complex-martini.top file? My command is as following:

"python martinize.py  -f complex.pdb -o complex-martini.top -x complex-martini.pdb"

By the way, is any script to generate Martini topology and structure files for lipids available? If not, how can I martinize a lipids bilayer?. Thanks.


More information about the gromacs.org_gmx-users mailing list