[gmx-users] Rhodopsin in membrane EM
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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