[gmx-users] About membrane protein

paulxie amianxie at gmail.com
Tue Jan 14 20:13:51 CET 2014

Justin Lemkul wrote
> You will have to position the protein differently if it is oriented 
> asymmetrically with respect the the membrane.  The same principles apply,
> but 
> box vectors will certainly be different, as will the editconf command.
> -Justin
> -
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to 

> gmx-users-request@

> .

Thanks Justin! It Is asymmetric because the protein consists of a
outer-membrane domain and a transmembrane helix. I placed the protein
asymmetrically to let the transmembrane helix in the middle of the bilayer
(dppc128) and adjusted the size of box. I confirmed that by checking the
coordinates in the system.gro and system_inflated.gro. But after that step,
after I did 
" grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1"
"mdrun -deffnm confout -nt 1"
the coordinates of protein were dramatically changed, i.e. the protein was
totally away from the bilayer. 
I think that should be something wrong, but cannot find it.

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