[gmx-users] membrane protein

strony_w_w_w at op.pl strony_w_w_w at op.pl
Wed Nov 3 21:56:13 CET 2004

Hi all!

I just started learning gromacs.  I need to simulate a GPCR in a lipid membrane.  

I did all the examples at your site, but still  have a problem:

At first I want to try simulating rhodopsin in a membrane.

      - I have  one pdb file with rhodopsin and some lipids and water after a MD simulation in NAMD (so all the coordinates are there) (I want to try it as a example)       

-         I did the topology file and coordinate file for the protein separately.

-         I did the topology file for  one  lipid separately and every thing seems fine. (prodrg)

-         I did coordinate file for one lipid separately. (prodrg)

My question is:

How can I combine protein and lipids and generate one *.gro  (coordinate file) for my whole system. 

How can I use my pdb file where I got all the coordinates for the system.

Should I treat every lipid as a separate molecule or as a solvent.

I would appreciate if you could give me some suggestions what should  I do next.  Thank you in advance. 
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