[gmx-users] Rhodopsin in membrane EM

Michal Kolinski mkolin at iimcb.gov.pl
Wed Nov 10 19:37:38 CET 2004

Rhodopsin in membrane EM

I'm starting to use gromacs.  At the beginning I wanted to do MD  of rhodopsin in membrane.  So at first,  I preformed EM of rhodopsin in membrane made of three different kinds of lipids.  (For coordinate file I used pdb file involving coordinates for whole system: water, lipids and rhodopsin.  This pdb file is a coordinate output file from NAMD after MD simulation and I guess it doesn't have any errors).  My problem is that after EM using gromacs I got very strange results.  In my output pdb file lipids broke into small pieces and the chain of the protein had a lot of gaps.  I used mdp file similar to this from speptide tutorial.  Itp files for lipids I did on my own, and itp file for protein I obtained using pdb2gmx.  During the EM I did not have any errors.  Maybe someone knows what could be the problem.  Thank you in advance.   Mike 

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